I have the same issue. It does that with my Shure wireless lav mics but not my friend's Senheiser wireless lavs. Then after reading posts where people had sync issues, lost audio with odd noises or gaps, and other recording problems, I decided to hook up a Zoom h4n to my Scarlet.
My Shure mics connect to the Zoom and gives me a backup to the Scarlet and also allows my Shure mics to work. I'm not sure why the Zoom with my shure mics work fine and why it doesn't on their own. Something with the circuitry or signal or frequency...not a clue.
It's not the best solution portability wise but it's safer having the backup audio. Still, I agree with Mark. Wish Red could just get this working...or better yet, have a simple add-on module that has XLR inputs (and nothing else).