Could it possibly be a "hardware acceleration" issue? Chess.com recommends disabling it.
https://support.chess.com/customer/portal/articles/1444971-how-do-i-fix-slowness-in-live-chess-
Don't suppose you're using a Wifi connection? I've read that some folks have solved problems by going back to a hardwired connection. Might be something in the following for you:
My apologies if you've already read the Help & Support articles, but you'd be surprised how many haven't...
Some time ago, i noticed my time running out while the clock displayed that it was on my opponents' time. I reloaded Chrome and the problem seemed to go away.
Recently, the problem has returned. I have experimented with pre-move and have actually lost 10s of seconds after making a pre-move <1sec after the clock shifted to my opponent.
This is not just lag. It happens with all combinations of good/bad connections with both myself and my opoonent.
What's up? How do I fix this? It is currently ruining blitz games for me.