Thread necromancy doesn't make for a wonderful first post I admit. But this is the first google result, nobody on the entire internet has solved this problem, and I found out something new about it.
First: The fix I used. Mount the SD cards under any linux distribution (i used a kanotix livecd). That's it. Then they'll work under Windows again. This worked for one of my cards and made it usable again, but not the other. It's strange.
Second: What a semaphore is. from
https://www-304.ibm.com/support/docview.wss?uid=swg21094630. Essentially a semaphore timeout means the multitasking is being pre-empted by something else on a fairly low level.
The fact that this is a card-by-card error, and the fact that chkdsk reports the filesystem as raw (my error was only upon file access, not entire disk access, but other than that the symptoms are identical), makes me believe a faulty SD reader driver is altering something on the card itself, which when read back, causes some driver process to to hang. This was later fixed upon mounting and dismounting it under Linux. Now, with both of my cards, my mp3 player (and Linux on the same machine) were still perfectly able to make use of them with no timeout issues whatsoever so this is very exclusively a windows driver error.
To clarify: After mounting it and dismounting it under linux, one card returned to a normal usable state, the other did not. Both were able to function under Linux, where I obviously backed up the data on each. I then backed up the data AGAIN under windows to make sure the timeout error was gone (it was occurring on SPECIFIC files, so being able to do a full backup under windows with one card indicated the error was gone).
This is with a Thinkpad T510 which uses the Ricoh 4-in-1 card reader, which I believe is the same one Sony uses in their Vaio line.