This was an issue for me prior to the last update, since then haven't seen it.
When I was having this issue before I'd just close the browser, re-open it and that would settle the problem in most cases (as long as Windows wasn't doing something in the background).
If I'm playing with someone who gets disconnected I get bad frames as soon as we resume. Same situation, just closing and re-opening the browser before I resume works to correct the frame drag.
Clearing cache should be a fairly frequent thing. WGT says only after updates, but it's easy for their junk to get corrupted on your machine. When you clear your cache you delete all old WGT assets (some of which are stored indefinitely) and re-download fresh new ones.
Having the most up to date images, assets and other things certainly helps. It should be your go-to move whenever something like that occurs, because chances are just doing that will fix it temporarily until something happens again. It's not 100% effective, but it's a good place to start.
It won't fix any problems with multiplayer, because you are depending on 3 other random people to know how to maintain their PC properly. Good luck with that.
Also, restart your browser after 9, 18 or 27 holes (or whatever it takes until you notice the frames starting to get choppy). Flash doesn't like running that long without a break.