General ⇒ Project interferes with other files

[whocares]

Hi,
I am using Texniccenter 1.0 for writing my thesis as well as from time to time writing letters with the university header and layout. After writing something again with the university-template I find that the letter is now completely distorted. I suspect it has something to do with the project for my thesis (book, A5, pdf while the letter is A4, letter and dvi-compiled.
Unfortunately the navigator in Texniccenter remains open with my thesis structure but my letter is not the main document of the thesis (makes sense).
Now the letter compiled perfectly before I started the thesis, no changes in the files since then so the only option is that my thesis-project somewhat interferes with the letter.
The question is now: How to I completely close a project and open another file fresh without having the rest interfer?
I made my letter its own project --> no, did not solve the issue.
I closed my thesis, deleted all unnecessary files --> to no result.
I deleted all unnecessary files for the letter --> no.
I cleaned up the project --> no...

Any ideas? Help would be appreciated, I do not really want to fiddle around with the crappy Word-university-styles from office 97 or so.

Thanks a lot.