Once you know what account it's trying to run under (the failure message will tell you), then you can right click on the SSMS shortcut and "Run As" that user (assuming you have the proper credentials). The server instance and the Agent need to be running from the same account. Also I think more recent releases of the OS have assigned the server administrator as the default SysAdmin account for SQL Server Agent jobs and then disabled those privileges by default. Furthermore, if you create a package in VS under a different user context than the one SQL Agent is expecting you will also run into permissions problems.
I gave up mostly trying to use the agent account for SSIS packages because it's such a pain in the rear unless one is the sysadmin of everything. I make my connections and linked servers all with TSQL code and just paste it into the job step directly. The security is not so hot if someone can get access to your box, but that's the only downside of using code I think but one with fairly low risk in most cases. Your situation will have to dictate the risk factors.
Here's an example of some code I use for running jobs. This one happens to use BCP to do a file transfer, but it's just an example of what can be done. I use it for some very complicated processes and you can even use it to run local stored procedures on your linked servers or execute a remote process on your local machine without the permissions muss and fuss of the agent service account.
USE LocalServer
GO
IF (
SELECT
SRV_DATASOURCE = srv.data_source
FROM
sys.servers srv
WHERE
srv.data_source = 'SQL-LINKED-SERVER-NAME,PORTNUM'
) IS NULL
EXEC master.dbo.sp_addlinkedserver @server = N'SQL-LINKED-SERVER-NAME,PORTNUM', @srvproduct=N'SQL Server', @provider=N'SQLNCLI'
EXEC master.dbo.sp_addlinkedsrvlogin @rmtsrvname=N'SQL-LINKED-SERVER-NAME,PORTNUM',@useself=N'False',@locallogin=NULL,@rmtuser=N'Your-USERID',@rmtpassword='Your-PASSWORD'
GO
EXEC master.dbo.sp_serveroption @server=N'SQL-LINKED-SERVER-NAME,PORTNUM', @optname=N'collation compatible', @optvalue=N'false'
GO
EXEC master.dbo.sp_serveroption @server=N'SQL-LINKED-SERVER-NAME,PORTNUM', @optname=N'data access', @optvalue=N'true'
GO
EXEC master.dbo.sp_serveroption @server=N'SQL-LINKED-SERVER-NAME,PORTNUM', @optname=N'dist', @optvalue=N'false'
GO
EXEC master.dbo.sp_serveroption @server=N'SQL-LINKED-SERVER-NAME,PORTNUM', @optname=N'pub', @optvalue=N'false'
GO
EXEC master.dbo.sp_serveroption @server=N'SQL-LINKED-SERVER-NAME,PORTNUM', @optname=N'rpc', @optvalue=N'true'
GO
EXEC master.dbo.sp_serveroption @server=N'SQL-LINKED-SERVER-NAME,PORTNUM', @optname=N'rpc out', @optvalue=N'true'
GO
EXEC master.dbo.sp_serveroption @server=N'SQL-LINKED-SERVER-NAME,PORTNUM', @optname=N'sub', @optvalue=N'false'
GO
EXEC master.dbo.sp_serveroption @server=N'SQL-LINKED-SERVER-NAME,PORTNUM', @optname=N'connect timeout', @optvalue=N'0'
GO
EXEC master.dbo.sp_serveroption @server=N'SQL-LINKED-SERVER-NAME,PORTNUM', @optname=N'collation name', @optvalue=null
GO
EXEC master.dbo.sp_serveroption @server=N'SQL-LINKED-SERVER-NAME,PORTNUM', @optname=N'lazy schema validation', @optvalue=N'false'
GO
EXEC master.dbo.sp_serveroption @server=N'SQL-LINKED-SERVER-NAME,PORTNUM', @optname=N'query timeout', @optvalue=N'0'
GO
EXEC master.dbo.sp_serveroption @server=N'SQL-LINKED-SERVER-NAME,PORTNUM', @optname=N'use remote collation', @optvalue=N'true'
GO
EXEC master.dbo.sp_serveroption @server=N'SQL-LINKED-SERVER-NAME,PORTNUM', @optname=N'remote proc transaction promotion', @optvalue=N'true'
GO
PRINT 'Exporting the pipe-delimited columns to local file.'
EXEC xp_cmdshell 'bcp "EXEC master..[your export proc]" queryout "C:\target.csv" -w -T -S"SERVER\INSTANCE" -t"|"'
PRINT 'Export to local file complete.'
USE LocalServer
GO
PRINT 'FTP to Remote Site site starting...'
EXEC dbo.UTIL_FTP_GetFile
@FTPServer = 'RemoteSite.com' ,
@FTPUser = 'RemoteUser' ,
@FTPPWD = 'RemotePW' ,
@SourcePath = 'c:\Remote Site\' ,
@SourceFiles = 'target.csv' ,
@DestPath = '\RemoteSite\Target\' ,
@FTPMode = 'binary'
PRINT 'FTP to Remote Site site complete.'
PRINT 'Start build of email'
DECLARE
@tableHTML NVARCHAR(MAX)
,@MailSubject NVARCHAR(75)
,@MailRecipients NVARCHAR(1000)
,@dateCompleted DATETIME
SET @MailSubject ='Export to Remote Site completed at ' + CONVERT(NVARCHAR(50),GETDATE(),120)
SET @MailRecipients = 'your.email@mailbox.com'
SET @tableHTML = ''
SET @tableHTML =
N'<H3>The following is the status for Remote Site Export</H3>' +
N'<table width= 70% border="0">' +
N'<tr><td align=left> 3) Job completed at '+CONVERT(NVARCHAR(50),GETDATE(),120)+'</td></tr>' +
N'<tr><td>
<td></tr>' +
N'</table>' ;
PRINT 'Sending email'
EXEC msdb.dbo.sp_send_dbmail
@profile_name = 'DBMail to OutLook'
,@recipients = @MailRecipients
,@subject = @MailSubject
,@body = @tableHTML
,@body_format = 'HTML'
PRINT 'Job Complete'
/*
CREATE PROCEDURE [dbo].[UTIL_FTP_GetFile]
@FTPServer VARCHAR(128) ,
@FTPUser VARCHAR(128) ,
@FTPPWD VARCHAR(128) ,
@SourcePath VARCHAR(128) ,
@SourceFiles VARCHAR(128) ,
@DestPath VARCHAR(128) ,
@FTPMode VARCHAR(128)
AS
BEGIN
DECLARE @cmd VARCHAR(1000)
DECLARE @workfilename VARCHAR(128)
DECLARE @workfile VARCHAR(128)
DECLARE @nowstr VARCHAR(25)
-- Get the %TEMP% environment variable.
DECLARE @tempdir VARCHAR(128)
CREATE TABLE #tempvartable ( info VARCHAR(1000) )
INSERT #tempvartable
EXEC master..xp_cmdshell 'echo %temp%'
SET @tempdir = ( SELECT TOP 1
info
FROM #tempvartable
)
IF RIGHT(@tempdir, 1) <> '\'
SET @tempdir = @tempdir + '\'
DROP TABLE #tempvartable
-- Generate @workfile
SELECT @nowstr = REPLACE(REPLACE(CONVERT(VARCHAR(30), GETDATE(), 121),
' ', '_'), ':', '-')
SELECT @workfile = 'FTP_SPID' + CONVERT(VARCHAR(128), @@spid) + '_'
+ @nowstr + '.txt'
-- Deal with special chars for echo commands.
SELECT @FTPServer = REPLACE(REPLACE(REPLACE(@FTPServer, '|', '^|'),
'<', '^<'), '>', '^>')
SELECT @FTPUser = REPLACE(REPLACE(REPLACE(@FTPUser, '|', '^|'), '<',
'^<'), '>', '^>')
SELECT @FTPPwd = REPLACE(REPLACE(REPLACE(@FTPPwd, '|', '^|'), '<',
'^<'), '>', '^>')
SELECT @DestPath = REPLACE(REPLACE(REPLACE(@DestPath, '|', '^|'), '<',
'^<'), '>', '^>')
IF RIGHT(@SourcePath, 1) <> '\'
SET @SourcePath = @SourcePath + '\'
-- Build the FTP script file.
SELECT @cmd = 'echo ' + 'open ' + @FTPServer + ' > ' + @tempdir
+ @workfile
EXEC master..xp_cmdshell @cmd
SELECT @cmd = 'echo ' + @FTPUser + '>> ' + @tempdir + @workfile
EXEC master..xp_cmdshell @cmd
SELECT @cmd = 'echo ' + @FTPPwd + '>> ' + @tempdir + @workfile
EXEC master..xp_cmdshell @cmd
SELECT @cmd = 'echo ' + 'prompt ' + ' >> ' + @tempdir + @workfile
EXEC master..xp_cmdshell @cmd
IF LEN(@FTPMode) > 0
BEGIN
SELECT @cmd = 'echo ' + @FTPMode + ' >> ' + @tempdir
+ @workfile
EXEC master..xp_cmdshell @cmd
END
IF LEN(@DestPath) > 0
BEGIN
SELECT @cmd = 'echo ' + 'cd ' + @DestPath + ' >> ' + @tempdir
+ @workfile
EXEC master..xp_cmdshell @cmd
END
SELECT @cmd = 'echo ' + 'mput ' + @SourcePath + @SourceFiles + ' >> '
+ @tempdir + @workfile
EXEC master..xp_cmdshell @cmd
SELECT @cmd = 'echo ' + 'quit' + ' >> ' + @tempdir + @workfile
EXEC master..xp_cmdshell @cmd
-- Execute the FTP command via script file.
SELECT @cmd = 'ftp -s:' + @tempdir + @workfile
CREATE TABLE #tempFTPGet
(
id INT IDENTITY(1, 1) ,
s VARCHAR(1000)
)
INSERT #tempFTPGet
EXEC master..xp_cmdshell @cmd
SELECT id ,
ouputtmp = s
FROM #tempFTPGet
-- Clean up.
DROP TABLE #tempFTPGet
SELECT @cmd = 'del ' + @tempdir + @workfile
EXEC master..xp_cmdshell @cmd
END
GO
*/