Same here. New update killed the ability to change the ISO in and out for Monster Rancher 2.
I actually bought this app just to play this specific game, and it appears the new update has stopped the ability to switch disks the way that it used to. All my ISO's still launch, but when I go to the shrine to generate a monster, it fails every time.
Also, the actual text has changed. It used to say "Reading disk information...", then it would switch to "Reinsert the Monster Rancher 2 CD". Instead it now says either "Insert CD" (after I had already changed the ISO), or (Checking the CD now...) and completely hangs up.
Hope this helps resolve the issue. This is the only game I play. LOL. Please let me know if there are any tests I can try.
EDIT: This issue is being addressed eventually. In the meantime try using the bare ISO's instead of those run through PocketISO per this thread here: viewtopic.php?f=39&t=2928&p=26563#p26563
EDIT #2: Apparently disk switching in ALL games is currently broken in the Android version of the app. So all multi-disk games, as well as games that use disk switching like Monster Rancher, are currently non-functional on Android devices.