Basically, all the FMLA does is protect your job with your employer while you are on leave. That's pretty much it: It means you can come back when you're done. It gives no provision that employers must offer compensation for time not worked due to illness/pregnancy/whatever. Whether you are pregnant or caring for a sick relative, the only way to receive pay for the time you are not working is to use up any benefit time which has already been accrued.

Sorry for agreeing with your admin on this one...