I have a similar setup and I have the exact same problem.
Ever since I upgraded to PS3 firmware 3.15, I cannot get video for any of my PS2 games through the Bose system, although I do get audio. PS3 games work just fine. When I plug the PS3 directly into my TV using an HDMI cable, I get video and sound just fine with both PS3 and PS2 games.
It seems that the firmware update has caused some sort of video incompatibility issue. We need to make them aware of this so they can fix it in the next update, because before this update, everything worked just fine for me.
If you find a work around, let me know.