To me, it sound then like audrey.abbey is likely correct...

Can you replicate the problem on another computer?
If you can replicate the problem, it makes me think the problem is not related to the end users computer.
If you...

A quick google of that error brought me to this:
https://technet.microsoft.com/en-us/library/ms187005(v=sql.105).aspx
basically - update SSMS, possible network issues, server setting may need changing (depending on the windows server version).

The database they were connected to had auto-close set to false, correct?  I believe that is a database level setting...  I am just thinking if they are running a query...

Is the client connecting from the remote site over some form of VPN?  Could there be an idle timeout in the VPN software?

When you that the connection is...

Well, the reason it is not returning results is your where clause.
since @Cat1 does not equal 0 AND @cat2 doesn't equal 0, one of your OR conditions needs to...

I think what Perry is suggesting (correct me if I am wrong though) is that your SAN team would handle everything with this.
They would migrate the data from the...

What about for answered threads, the thread title would have the text "ANSWERED" after it.  So for this thread (presuming it was answered), it would say: "answered" thread...

Good to know.  I thought it was working since the patching.  Which, while true, has not had a long enough runtime to verify that it is "fixed".

Could it...

I would expect, since it is getting "access is denied" errors that the problem is with a specific account.

But I suppose if things are running now, it might...

If you execute the stored procedure as the SQL Agent user, does it execute successfully or do you get that same error?

Since it has run successfully 3 days...

Good to know.
Brings up the next question though - what is different between those 2 configuration files?

Also, was re-reading the initial post... how does the JOB call...

Ok, so my next thought is what is different between the 2 configuration files you are using?
My GUESS is that they are pointing to different SQL Instances or databases. ...

Adding to this, what does the "All Executions" report look like for that SSIS package (presuming you are using an SSIS catalog)?
Might not hurt to turn on verbose logging...