Texmaker and TeXstudio ⇒ Odd error in texmaker?

[qwasd]

Hi,
I'm using Texmaker 3.4.1 in Windows xp to write my thesis

if I double-click Thesis.tex, it automatically opens via Texmaker. If I quick-compile I get "Log file not found", or occassionally it appears to be compiling but produces no PDF.

If I open Texmaker FIRST (ie no documents open), then either drag in Thesis.tex or File>Open, everything is perfect. I can compile/view pdf/make bibliography etc. all the references seem to be working.

Has anyone seen this? I guess it's not that important, but I can't figure out what the problem is and it's bugging me a little. I have a batch file set to automatically open Thesis.tex, Chap1.tex, Chap2.tex, etc etc and it's currently not working because it does the equivalent of double-cliking the file directly. (However it used to work fine. Not sure what's changed though!)