had the same issues and automatic gamefixes didnt help - but I managed to play thru the whole game with several changes of settings.
You will later enocounter a level (volk city) with another big issue. This cant be fixed with just a setting -you have to install a patch. Didnt know about that and how it works until I had to do so. The Patch including all instructions (patch must be saved in the “cheats” folder of pcsx2 emulator) is also availabe at the PCSX2 forum. I used it and was able to complete the game.
Best source is the pcsx2 wiki for Klonoa2 - your Orb Problem can be fixed with following setting:
…You can manually enable the fix by going to Config > Emulation Settings > EE/IOP tab, and setting EE/FPU to “Nearest or Negative” (copy&paste from pcsx2 wiki)
Hope that helps you somehow.