Yeah I have this too, with both TS 12 and TANE. John is right in that it affects JR's locomotives especially, but it is an overall problem. For me it happens notably after I save and reload. I can drive a long route, say UMR for 20-50 miles in one shot and not have an issue for the most part. But once I stop, save and reload, the sound deteriorates with each save and reload to where after 2 or 3 , the game becomes totally unplayable for me and I just quit the session in disgust.
I thought at first it was something with my system and TS 12, I use onboard sound, but it also happened once I started using TANE. I thought maybe that once I upgrade to a new computer that it would fix things but seeing how others are having issues I'm not so optimistic. I've pretty much decided to stop playing the game until I get my new machine, but if it is going to continue I may just not even bother until it can be fixed, if it can be at all.