Nonsense. It was black magic ya here!? wink

Yea ok, it was that simple. I need to split my gameboy into two channels, I thought the interface could receive in stereo. *loosens collar* I feel embarrassed, especially when I thought I was "definitely" not recording in mono.

I'll buy some cables to get that happening and get back to you if my problem still occurs. Thanks for your help. I feel stupid, lol.

M Audio Mtrack.
I'm going to try see whats going on in audacity. maybe i AM recording in mono but dont realize or something, Im going to rule that out before I go to the effort of google drive wink

Definitely not recording in mono. Just seems like audio interface doesn't like 'raw' gameboy signal
What is the best means for getting some audio online quickly?

Same cable used in both cases. regardless, I can confirm recording from phone to audio interface, headphone out from gameboy and gameboy to external amplifier are all working fine. But when the same gameboy signal goes to the audio interface it is missing half the information and is all weird e.g. wav channel will be muted and pulse channel will be triple its normal volume in some parts. However, when buffered through the busking amp it works fine. Have tried different gameboys, different cables, same cables etc.
You can literally have the song playing and switch output devices while its playing using the exact same cable and get two different results. do you record your DMG?

TL;DR version is basically describe the recording setup you use for capturing your tracks off your DMG. For those who cbf, here is my story below...

Hey all, I'm a bit of a noob. Ive written a bunch of tracks on my DMG and Im ready to record.
When listening to my tracks through my audio interface it seems like half  of the track is muted or clicking, some parts have the completely wrong envelope, some are half volume, all sorts of random things that sound nothing like what I had written when you listen through other means. I have tried several gameboys, some were prosound modded and some were not. Through all of them, I do not get an accurate representation of what I wrote when plugged into the audio interface directly. 
It is only a recent issue, as up until I planned to record these tracks I was listening to them live through a roland busking amplifier with a line in. Now interestingly, when I plug the gameboy into the busking amp, then use the line out of the busking amp into the audio interface none of the problems arrive and I can actually hear my track.
So what is going on here? What black magic is occurring by buffering through the busking amp first?
One would assume it is normalizing the level or strength of the signal in some way. How can I get this result without buffering through the busking amp?
Would a normal 4 channel mixer get the job done?

Any help figuring this one out would be greatly appreciated.