I didn't see where you tried rebooting the pc? Tried a different pc? You could walk into any store and plug it into the usb port of a laptop on display.
Reboot with device connected might work, and good advice to try another XP (or two) to see if something with the MT has gone south. Re-installing the latest firmware (again) should be tried if all else fails. And definitely get a 2.0 USB card reader as this will usually transfer files far faster than the deck's connection.
A little off subject, but may be of interest is I have concerns with continually using a reader. Issue here is the CF card connectors wearing out with hundreds to thousands of removal/insertion cycles. These connectors are very tiny, and will wear out eventually, but after how many times is the question.
It does make one think about continually removing cards from the deck for transfer.
I admit to not researching this question, and need to do some search for contact cycle life on these devices at first opportunity.
Since no one has complained about Flash card connectors failing that I've heard, likely not a problem for many years.
My concerns on (all) connectors gold plated male/female contacts is lint/grease contamination, wear out of the gold plating (very thin in some cases), and female contact finger-pressures getting too loosened for reliable contacts. Therefore suggest applying a good contact treatment on audio/video/digital connectors that get handled and cycled.
In any case, for may years I've virtually eliminated plating wearout and contamination sticking onto the metal with using Caig Labs DeOxit ProGold treatment on the deck's connectors/patch cables, and on all the flash cards I own or send with system packages to customers.
I brush a little over the flash card connector and use light compressed 'clean-air' to 'blow' some into the connector holes where the contacts are recessed from direct brush application, then wipe the excess of with lint-free cotton cloth or use air to blow off excess leaving a thin film that lasts for many years. There are spray versions of this product, but found the spray is overkill for what little is needed, and can go where no contact lives to maybe cause problems with DAT drives or MD optical systems, so the manual brush is most wise and economical.
One thing I do like about R-09 deck's use of SD flash over MT's CF cards is while the SD cards are quite tiny, the contacts are HUGE in comparison to CF. Maybe CF cards use redundant pins so many small contacts are used instead of just one tiny little pin for critical connections? If so, then CF card connections may be just as reliable and long lasting as SD flash's large contacts seem to be.