Chosen Solution

I used to be able to play PS2 games on my backwards compatible PS3 but now they load but the controller no longer lets me use the start button to start the game. The only difference i know of is that I recently updated the software in the PS3. Is there a fix for this?

Yes, after launch the game (ps2 game) please press home button on your stick to connect with games. If not work use cable and plug then press home button again.