Is there really no fix for issues like this other than using software mode? The problem is, in software mode some scenes and battles are very very slow. *sigh*
What are your specs? Have you tried setting extra rendering threads for SW mode?
Well this is my PC specs, I believe its good enough to run any PCSX2 games that are internally compatible:
Processor: Intel i7-4800MQ 2.70 GHz (x 8 threads) | 3.70 GHz (x 4 Threads) | 6 MB L3 Cache | 47 Watts
Graphics: nVIDIA GeForce GTX 765M 2GB GDDR5 | Display: 14" FullHD 1920x1080 LED Screen
RAM: 16GB (2 X 8GB) DDR3 1600MHz 1.35V | Hard Drive: 1TB 7200rpm HDD | Optical Drive: SuperMulti 8X DVD+/-R/RW Dual Layer (Slot Loading 9.5mm)
You should be able to handle software mode with that. Set extra rendering threads to 3 or 4 in GSDX configuration and then try software mode.
Have you tried to run it in Hardware Mode + Native resolution?
A lot of these bugs are caused by upscaling and should work fine in hardware mode too at native resolution.