geez......what a great forum this is.........
First you ask a question on the weekend when most people are not in the office. Second, you ask a question that is not a common setup for most. I dont know what you expected to happen.
Anyway, I dont see a problem in what you are proposing. If you use Parallels to capture the image where do you plan on storing the images? Are you even storing them in the container or just using a reference to them? If so, obviously you would need to have a common access to that location from all your client sessions.
If your medical card scanner scans a magnetic strip it may well be possible to get a mac compatible scanner. USB is a common interface for such hardwared and in keyboard emulation mode it would (I think) function identically for both platforms. You could place the cursor in your database field and the text from the mag strip would be read and entered into the field just as though a user had typed the text in.
A "post amble" can be programmed on many such devices to append text to the end of the scan. You can set up a script trigger (FMP 10) or simply pause the script in an endless loop (pre FMP 10) to detect the post amble text and thus respond to the scan action.