I would assume that your latest firmware update was version .015. I have the Sony BDP-S350 as well, at version .015 (updated from version .010, updated from the original factory version .007), and have not had any problems. I don't have a ton of titles, but I've had no playback problems. If you are running firmware version .015, then you should not be experiencing any disc incompatibilities.
As you suspected, the insertion of the thumb drive does not affect the unit's playback operation.
Sounds like you might have a bad drive in your player. More specifically, it could be a defective laser or pickup. It could be as simple as a dirty laser lens. Not sure if you can use a CD laser type cleaning disc in a BD player, but it may be worth a try.
Lastly, if you can, take your Mad Men discs to a known-good BD player (perhaps a friend's, or even a local audio/video store) to make sure they are fine.
Best of luck to you! The S350 is really a good player!
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