Hi, we did find a way around this. If the .ino or .pde sketch file is double clicked and the Arduino program opens, you can have two independent Arduino windows running and can use one for the UNO and another for a Mega128 board. We did just this and managed to get the two RF cc2500 modules talking to each other.
The original problem happens if a new Arduino window is spawned off an existing one, by selecting new sketch. I cannot imagine any situation where you would want two Arduino windows talking to the same board so it would be good if this could be changed to be independent. Anyway, thee is a workaround.
Also, we noticed today that Arduino was taking a while to startup and this was caused by having three old IDEs still installed. I think Arduino scans all the directories for sketches on startup. Removing the old IDEs dropped the startup time to 10seconds. Btw, there was no difference between v0022 and 1.0. Thanks.