Why are you splitting the alpha and background into two separate files? The correct way to do it would be to record it in a single file with a codec that supports alpha, like Cineform or (possibly) DNxHR. PNG might work as well.

I tried cineform,  its just BG file without Alpha. 

Maybe I misunderstood what you’re trying to do? Are you sending the keyed foreground with alpha on the second output? 

If you’re not working with live video you could just set an exact frame rate for both recorders instead of Real-time. 

I'm shooting a virtual production project. I have my final compositing recorded in Blackmagic video assist 4K  but I also want to record from Aximmetry separately BG and Alpha for further post production correction, etc. That's why I need all 3 separate recordings. And apparently Alpha file is in 24fps and not 30. 

Hey AVRJapan, i assume you are recording the final clip in real time and not as playback? 

If so, try setting the alpha to record to H264 instead of png, the issue might be with the fact  that you are writing 30 separate files/second to disc and something there is messing up the sync (I'm not sure, but i always record alpha to external file and have no issues) 

H.264 should have no issues because in the end the alpha file is just a black & white mask and you can just use it as an alpha matte in basically every post production software & you will save a ton of disc space as well. (If there are compression issues set it to Cineform)