I discovered, that the BM wont delete the directories when uninstalling an app and found a small bug in your megapack-scipts which causes the prob:
Originally Posted by TheAgent
RMDIR "$SRC_PATH$/MCMGR" cant work because the SRC_PATH is the folder with the app in it and the one you want to delete.
Changed it to RMDIR "$ARG2$/MCMGR" and now it works. RMDIR "$SRC_PATH$" should work too, but I did not test it.
Would be nice if you could fix this with your upcoming new megapack.
You can install uLaunchELF via BM and use it to transfer myPS2 and all the subfolders from usb or cd to your MC (BOOT/APPS/MYPS2). Copy the APPINFO.PBT attached here to the MYPS2-folder. Then you can run myPS2 from BM. Only for install and uninstall you have to use uLaunchELF.