posting to this thread waaay late, however I just had this problem yesterday with an Omnikey 3121 reader on my Win 7(64bit) PC.
When plugging the card reader into my PC, the OS automatically loads the appropriate microsoft plug and play drivers
The Log Card Utility from Concept2 then recognizes the reader, but when inserting a card, the utility cant see it.
to solve this, download the drivers from OmniKey http://www.hidglobal.com/drivers?field_brand_tid=24&product_id=All&os=All
go to START->Devices and Printers->open the Smart Card Reader USB->HArdware tab->Properties->driver->Update Driver, then select the extracted driver package you downloaded.
Apparently, the microsoft drivers dont work with the Concept2 utility.