I am running the svn-1025 version of Firefly (from the "nightlies" website, rather than as renamed as Beta3 and available from Roku - so I hope it is identical and my advice to you here is correct) and it definitely supports WMA music.
Maybe the installer doesn't include WMA as a supported filetype in the Firefly configuration file by default? I edited my configuration manually (as below) when I first installed Beta 1 and it has stayed that way since (ie through several build update installs), so hopefully this will be a one-off setup item for you too.
Go to the Advanced Configuration option under Firefly in the Windows Start menu (this will open Notepad on the configuration file) and there is a line in that file which lists supported file extensions. Add .wma (with a comma in front) to that list and save the file. NB: You might have to stop Firefly, delete the songs.db file and then restart Firefly again for it to fully rescan and pick up your WMA files but it should be happy after that.