as far as I know if you have different arduino applications open whatever you set in one will be the setting in the other, though it may not show it
I ran into this not too long ago where I was developing on a mega, but the final target was a 328P device so I opened up another arduino IDE, loaded the arduinoisp sketch to the 328, went back to the mega window attempted to upload a change and got an invalid device signature error from the mega, which the signature was for the 238P.