Well, I do not fully understand your problem, but there are some things that are special for me (I'm using a Wacom aswell):
1) If I start up Gimp with a mouse-click, it does not accept any inputs from my wacom.
2) If I change any tool options with my mouse, they do not apply for my wacom.
3) If I change any tool options with my wacom, they do not apply for my mouse.
So using the mouse to change settings will change them as long as your pen does not touch the wacom. The settings will be reset to the last settings used with the pen.
Just change the settings with the pen in your hand, don't touch the mouse, and the settings will apply to the pen.
Hope this helps.
David Wood wrote:Arzorac
Cyrilshark wrote:Argzornack, I still have to congratulate you on having the most epic signature ever. haha