Background:
I built an installer for my app, and all my dll\'s and content files are getting correctly copied to the C:\\Program Files\\MyComp
Use Application.StartupPath instead of Environment.CurrentDirectory.
I've had a similar problem, where the CurrentDirectory was being changed inadvertently by something like an OpenFileDialog without me even realizing it.
In your case, it sounds like the process that you're starting the application form is changing the CurrentDirectory unbeknownst to you.