In your eqclient.ini there are several different options that control your resolution, with one set for "windowed mode", and one set for "full screen mode". It sounds like you need to edit the ones for full screen mode to match your windowed mode.
However, I'd suggest that you what you probably
really want isn't full screen (that's so 1999
[You must be logged in to view images. Log in or Register.]) ... but rather the best of both worlds, ie. "full screen windowed mode". With that approach you
technically are in windowed mode (and so can easily switch to other programs), but you tweak your windowed resolution so that it takes up the full space of your monitor (minus a sliver at the bottom for your task bar).
For details see:
https://wiki.project1999.com/User_In...ndowed.22_Mode