Usually when you put the disc in and click on the game icon in the xmb, it installs gamedata to the harddrive and then when the game is going to start, it says something about needing to update the system software. Then you have to click on yes or no. That's if the game requires a higher number firmware than what is on your ps3.
I haven't played any games higher than 3.41 (or maybe 3.55 can't remember) so don't know if it's changed to silent update automatically. Also, I guess probably don't want to be connected to the internet when using one of those games.
Do some tb versions have a spoof (of the firmware version)? Just wondering if that could be part of the problem. Obviously no playing of tb games with MM without the dongle.
Finally, not a good idea to have a game disc in the drive when you install firmware cause sometimes the ps3 decides to install what is on the disc instead of what is on your usb stick. Sorry for your misfortune.