How to Upgrade from Windows Vista x64 to Windows 7 x64

I will bet an honest Abe that it found a driver in your Vista 64 bit that isn't signed by "Microsoft Windows Hardware Compatibility Publisher", and the Windows 7 installer is complaining about it.
And in order to make sure everything works after the upgrade, it will warn you.

Wither or not it would be safe to continue, I don't know the exact answer. If you have data you want saved then I would make an image with it with some program like DriveXML or http://selfimage.excelcia.org/ ...otherwise if you can stand to lose whatever data you had on it, then try it anyways.
I am not saying blindly leap forth, but if you can't find a newer driver, then backup and try continuing anyways.

I have performed the following steps and now the problem is solved!

1) Disconnected Media Card Reader and reconnected it. I wanted Windows to automatically detect the hardware change. Details of the first step:

a) Turned off Windows.
b) Disconnected Media Card Reader.
c) Turned on Windows.
d) Turned off Windows.
e) Connected Media Card Reader.
f) Turned on Windows.

2) Disabled and re-enabled the controllers.

a) Opened Device Manager.
b) Expanded IDE ATA/ATAPI controllers.
c) Uninstalled each item one by one.
d) Restarted the computer.

3) After the computer started, Windows reinstalled all the controllers that I've uninstalled. I've inserted a SD Card to the Media Card Reader to see whether it was working. And voila! It was working.

The only difference with Vista is: I cannot see the drive letters in My Computer unless I insert a media into the reader. In Vista, I was able to see the drives even when there is no media in them. Maybe this is handled differently in Windows 7, or related to some adjustments, but it's even better for me.