Just to be sure, is the config file with the user credentials stored in the same directory as the package? Are the package and config files in a shared folder that both agent and the user credentials in the config file have access to? I ask because when it works in BIDS and not under agent (not sure if this is all the time you mean or part of the time)... you have to rule out that the solution you created is still not in the visual studio projects folder under your name.. ie...

C:\Users\yourUserName\Documents\Visual Studio 2008 ... where an agent or other user may not have access.