Alright, more information; I did some digging and testing.
When I open mGBA, close it then remove qt.ini, I am able to start the application with no problem. And it works no matter if I remove the files or not. I have no more issues. I tested it a few more times to reproduce everything. If I leave qt.ini and try to re-open it I get that error message, even if I close and remove qt.ini. I am unable to start mGBA at all until I delete all 4 of those files and re-open it, close the application then remove qt.ini. This happens consistently. I have found a workaround for me so I hope this helps others who may have the same issue. I don't know if this is a specific issue just on my machine or what, but at least I figured out how to use your emulator and when I get home I can finally get my pokemon fix on!
Edit: Edited for clarification.
When I open mGBA, close it then remove qt.ini, I am able to start the application with no problem. And it works no matter if I remove the files or not. I have no more issues. I tested it a few more times to reproduce everything. If I leave qt.ini and try to re-open it I get that error message, even if I close and remove qt.ini. I am unable to start mGBA at all until I delete all 4 of those files and re-open it, close the application then remove qt.ini. This happens consistently. I have found a workaround for me so I hope this helps others who may have the same issue. I don't know if this is a specific issue just on my machine or what, but at least I figured out how to use your emulator and when I get home I can finally get my pokemon fix on!
Edit: Edited for clarification.