I'm sorry to say that I've never seen this problem, but in all honesty, it could even be due to JFW, as it's known to be a resource hog.  That's the only thing I can really think of but I hope you manage to get things fixed.

If you were to look at your task manager, you would find that JAWS processes are still running, such as the FSAtProxy.exe process, which never seems to go away unless you personally terminate it.  While it alone may not be causing the issue, other processes might be refusing to quit, thus making your computer crawl as slowly as it does.  You may find this hard to believe, but on 3 windows 7 machines I've already had more issues with JAWS than I can count, all of them concerning the very same thing, that being remote procedure call. Symptoms which you may find in some of my other posts on this forum follow:
I run JAWS for awhile; I do any number of things with it from troubleshooting other people's issues to helping people figure out its apparrently complex layout... I think we've gotten much lazier over the years and for whatever reason best known to ourselves can't be bothered learning instructions, but that's a different subject for a different topic.  I close it and relaunch NVDA when I'm done with it and hover my cursor over a .txt or .rtf file.  NVDA trys to present the information concerning the file such as the date it was last eddited, created, the size, etc etc.  NVDA never manages to present the information owing to some manner of interference I can't quite pinpoint, but which I'm certain has something to do with JAWS because it never happens at any other point in time.  Windows explorer stops working and must be restarted.  After restarting, some 30 minutes must go by or the PC must be restarted altogether before I can access anything on my PC with the exception of other software.  Trying to boot into any of my drives or attempting to launch them or any folders from desktop shortcuts result in the error message, "The remote procedure call failed and did not execute."  Three different computers, same operating system, same precise patern.  No, this isn't me hating on JAWS; this is me pointing out something people gloss over.

I can't speak for Jaws, but I haven't seen this problem myself when around between nvda and supernova.
indeed yesterday I made a total booboo and in my forgetting which key bought up the esp pinball registration dialogue, by mistake activated supernova while and esp pinball were both still running.

I was actually quite impressed with how Nvda handled this, Supernova didn't speak directly, but Nvda switched to the next orphius voice along (supernova was using Alan and I suspect both screen readers couldn't speak at once because both were using orphius), I was then able to get to the sn control and close supernova, close esp pinball, then just reset the nvda voice to Alan and everything went fine.

i have had the same exact issues with jaws as Nocturnus. it made me officially switch from jaws and now i only use nvda on windows.