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I may be mistaken on this, but I believe VRC7 is only supposed to be able to play one custom patch at a time, so if you have one in one channel and a different on playing shortly after in another, the second will cut the first on off. As for multiple of them being triggered at the same time... I have no idea.
Edit: Yeah, I think that's the issue. I've attached a slightly modified version, switching out channel 5 and 6's custom patches with normal ones, and none of the notes are cutting off.
Before you try Je_mappelle-ing, you should really get to know your VRC7, and you also need DPCM mastery, and a fairly great knowlegde of house/dnb, plus throw in a little bit of experience with working with a higher number of channels.
EDIT: Yeah, a ton of channels are space-abused. You need experience with using that much space properly.
Just act as if you are still very limited, but reduce the limit-feeling factor by about 2 channels. Don't go out on Famitracker VRC7 like you would MODPlug FM VST's.
I think the custom kick isn't really enough to propel this tune. It's got the low end pretty well, but it's lacking a poppy high end that's standard for prog house.
I'm not too sure how well DPCM handles a clean pop, but give it a go.
Also, I can synthesize a .wav if you need one. (my other musical endeavor is making EDM)
[edit:]
Okay just tried with one of my kicks, and it does not convert to DPCM well
Though it does give it some mid range (you'll probably have to EQ out the low end of a sample), a simple Z00 gives it the proper high end.