It could be a service that is not starting automatically, or drivers that are not being loaded at boot time.

There are some things you can try:

1. Check Services to see what is running after a cold boot. Then, when you get the card reader working, check Services again to see if anything else is not running that wasn't before.

2. Check Event Viewer to see if there is anything that is failing to start when you boot.

3. Try booting up with a card in the reader to see what happens then.