I think DXV has no chance to screw up things on that side, is just AE.
Check if you're rendering with Premultiplied (matted) instead of straight alpha.
I bet you're premultiplying by lime, tasty but wrong for alpha creation.
I personally don't think a scrollbar is the solution for this. I think the layer scroll buttons should be more responsive, and when you hold them the should scroll the deck list speeding up, so you don't need to click much. Holding a button can reduce clicks, but is a way to SLOW things down. Multi...
Try this, a simple fx clip with levels (I've added color to notice it in snapshot) with a simple jpg mask.
Then enable the Layer 'ignore column trigger', not in the clip itself.
I encorage you to download resolume and test it by yourself. :D You can do it in the same way, triggering a clip from midi note can have some latency, but in order of a couple of miliseconds (has zero delay for me). If you're syncing a clip with a premade track, think if you can send a smpte signal ...
