Original dlls are affected when running a sub process separately

I am working on a Windows application designed in vb which has quite a number of modules which get attached to it via reflection. The each module also has a embedded sql file attached to it which gets executed when the user logs in. I was trying to execute these embedded sql file using a separate console. So i extracted the code and built a Console App. The app execution is failing for some modules where i think i might have missed something. The problem is when i go for the actual app after the console app execution the failed modules also fail in the actual application. I am not sure why? In a clean setup the original application has no issues. I am not referencing anything from my console app to the original window application or vice-versa. The application is running on version specific dlls. Can someone help me out in pointing to the right direction ?