Welcome to FT afhstingray!

Yes, the expiring miles will be the first to be used up.

At what stage of the process does it say the flights are not available? When I log in on emirates.com and search for awards, it shows me the availability for different awards on different flights and I'm able to select flights and view the screen with miles + taxes. Have never gone beyond that screen though. Maybe you should call up Skywards if you continue to have problems.