If you are referring to Indivision AGA mk3, then that is not a graphics card, it is a flicker fixer/scan doubler that just alters the video output of the original AGA chipset.
PerfectPaint wants high colour (15bit, 16bit) or true colour (24bit, 32bit) screen modes, and for that you need RTG, that is the Picasso96 or CyberGraphX software, with supported graphics card hardware.