I experienced the same thing when I use the SD card stereo record feature. I have to boost the wav files in Pro Tools.
It works but not ideal. Sometimes the results can get noisy when boosted.
Mostly it works OK as a scratch pad.
My biggest problem so far is trying to get a computer to run univ control or capture 2.
I tried a mac and it was too new. Now a PC running Win 7 and the univ control driver does not load.
My patience for the AR16 is running out. It's a nice board, but may not pan out for me in the end.