Disappointing!
But at least you still have all your files intact.
Out of curiosity too, did you connect the card reader to a USB3 port(or USB2 port)?
I assume it was a USB3 port(on the PC).
If so, maybe try test with some random files on a CF card but this time using USB2.
I once had an issue with a new USB3 device(docking station for a HDD), kept stalling at some point during transferring data(1Tb+)
Didn't realise it at the time, but where it stalled it also corrupted some files, so I lost a few(maybe 20 or so) NEF files.(turns out they weren't important, and would have been deleted anyhow).
eventually found out why it all happened .. docking station ended up "hacked to tiny bits" for the purposes of greater knowledge of microelectronics .. and a new docking station was bought(that works flawlessly).
So my thinking is: if you do try the USB2 test with the reader and it does work properly, then the card reader is junk(as in should be junked!) .. it's almost certain that it uses the same JMicron chip my docking station used, and no amount of firmware updating will make it work.