I just used a memory card from my camera and put the update on there, plugged it into the reader in front and it worked fine. Just have to put it in the folder, same as on a CDR. Quick and easy.
Well, I tried Kingdom of Heaven which also has a Master Audio track via optical and it sounded great.
I guess that is why I've never seen that problem, since I always just use the PS button to go back to the menu or turn off the system when I am done watching.