I'm running OSX and recently upgraded my IDE from 1.0.5 to 1.5.7 to use the Yun and am experiencing the delay issues both on startup and when selecting the Tools menu. I also tried older 1.5.x builds and had the same issue. I don't have any problems using 1.0.5 and an Uno.
I attempted to follow the instructions but haven't been able to figure out where to place the updated files. They don't appear to already exist in the lib folder when I look through the Arduino package in OSX. I searched my computer and couldn't find a file with RXTX other than the ones I downloaded using the links from this thread. As an alternative I tried to place the files in the Extensions folder in HD/Library/Java/Extensions but to no avail. I also tried turning off Bluetooth which had been suggested in other threads.
Any suggestions would be greatly appreciated.