RetroFW 2.0 has also other issues (including one where they seemingly moved $HOME to another location which can't be written to or has permission issues) so i would hold off on updating to it for now.
Actually $HOME is quite writeable... it can also be moved to any dir, internal and external by users from Settings' HOME PATH setting.
I'm not sure what's the problem with your OPK build of PCSX4ALL.... I can tell the previous IPK one still works perfectly and saves everything correctly (as do all the other emus/ports apart from Cave Story OPK, which is trying to write on its own directory -not on home- and that's obviously impossible with an OPK... just use the IPK for now).
It also seems to be pretty prone to crashing, especially when entering the menu... and most often I can't even enter the menu itself: you might want to fix it. In the meanwhile I'd suggest users to just use the IPK, which works perfectly as it always did.
PS: IPU scaling seems to be working perfectly though... nice.