I can play WMA files in MusicMatch Jukebox (which I use), but I can't play FLAC files.
You must be aware by now that MMJB is an end of line piece of software that will receive no future development. Musicmatch was sold to Yahoo some time ago and their service (and customer base) is being transferred to Yahoo Music by the end of summer. Most recent development in MMJB was geared toward adding features for selling online music so it is little wonder that flac was not added. I hope you didn't get conned into paying $60 for future upgrades of MMJB because there will be none. Just one of the pitfalls of buying proprietary software. Personally, I prefer Winamp. It does everything that MMJB does, is a lot faster than MMJB for large music collections and supports virtually every music format in use through user developed plugins. For ripping, I use Exact Audio Copy. It also supports virtually all file formats through external add-ons. I tried MMJB for ripping but got too many bad rips. My MMJB+ license and Musicmatch subscription are also up in the air because I have been unable to get Yahoo Music to transfer my subscription due to being in Canada.