How are you setting your environment variables?

Where do you store your values (table, XML Config file, etc.)?

What string are you using to call the package and what is the package calling instead of the values you us in the string?

There are two possible explanations to your problem. 1) Overriding variables or 2) missing config file.

1) I don't remember the exact details, but a few years back, we found out that SSIS re-applies certain variables after those variables are "called" in the SSIS execution string. This happened before we started using XML config files. Once we switched over to those, we seemed to have had no problems. Well, except for issue #2, that is. @=)

2) Say I have pkgA and I created it on my PC, creating a config file under the path C:\ConfigFiles\MyConfig.dtsconfig. Then I move it up to Production and call it using \\ProdServer\Production.dtsconfig. Now if Production.dtsconfig doesn't exist, SSIS will default to looking for the config file on my box (assuming it has permissions to read that folder). And if it doesn't work, then it will read the hard coded values in the package.