Not just, no... the music tracks playing on a loop most of the time and not really synching to the scenes is also an issue, because then you can get a track that absolutely doesn't fit the tone of the scene.So I presume you are referring to music cutting out when animations start? If that is the case then it's because the animations are cut-scenes (which seems to be the worst possible option). I'm working on transferring the project to renpy v8, and hopefully cleaning everything up before end of the episode. I'll also make the text box opacity adjustable (added it because even with outline, some people could not read the text at times). I hate the coding part, so I kind of have to push myself into doing it...which is why it will take a bit
The whole music side of things needs a lot of work in general, I think you need more tracks, maybe add some SFX, and perhaps also look into using more background ambience tracks for certain scenes, so as to not always use BG music (like the jungle sounds in the flashbacks).
Oh and yes, making the opacity adjustable would be the best probably.
One last thing, I noticed a lot of choices are mostly for flavor and don't really have an impact, sometimes it's more notable like when you choose to stay in the bar instead of going after the pawnshop owner, and then when you go to the next scene in the office, the MC still reflects on the events as if he'd gone after the dude no matter what... Same goes with the bald gangster's mom and how being nice or rude to her doesn't really change her reaction later on.
Flavor choices are fine, it's just that if you have different info or interactions because of them, then that should be reflected later, otherwise it's just strange and doesn't quite make sense.