I noticed that the NTSC filter plugin seems to have been updated since Regen v0.95. The problem is that the current version displays screwed-up colors until you open its configuration window and select one of the preset configurations. If I replace it with the NTSC plugin supplied with Regen 0.95, everything works fine.
Remove "ntsc.ini" from the plugins directory and try with the new plugin again. The plugin packaged with 0.96 is the one available from 
here. So it has been slightly updated. If all else fails, try to download and use the filter from the link above (but remove ntsc.ini as from plugins directory).
Also, when lockup emulation is enabled, Sonic Crackers causes the emulator to quit unexpectedly at the point where the lockup should be triggered. The usual Windows error ding sound plays, and some dialog box titled "Fatal Error" flashes very briefly. 
I previously hinted at two other games which trigger the lockup emulation. These are "Iraq War 2003 (Unl)" and "Deer Hunter (R)." They do not cause an unexpected exit; instead they cause the previously mentioned undesirable behavior where the "System lock-up!" message is displayed an infinite number of times and the lockup state cannot be cleared by loading another ROM. There is a new regression involving these two games, which is that they fail to produce any sound. (These two games are unlicensed games based on the Tomsoft Studio SEGA Kit, and their sound is entirely PCM.) 
I don't know how I missed to fix these bugs 

 . Thanks for reporting these will be fixed for sure in the next release.
I tried Blarg's NTSC filter and it totally killed the performance, making the games unplayable with audio on. This is probably again caused by the Athlon 64. I was curious what the filter did though, but didn't see any noticeable difference on the RPTV. I haven't had any luck with video filters in Gens Surreal either, they all seem to kill the performance in both of my PCs.
That filter applies NTSC video signal processing on an image giving a result very close to a console connected to a TV. The filter is a bit heavy but it shouldn't make games unplayably slow on your configuration. Hmm....maybe Regen got more slower than I expected. I have tested it on a single core Pentium 4 2.8 Ghz (w/ onboard Intel graphics) and it runs fine. I'll research a bit more on the problem.
I also tried some SMS games. Having not ever heard the YM2413 chipped games on the actual console I can't comment on audio accuracy. After Burner's title music had a very repetitive beep in the background that I haven't noticed in Fusion or Meka. I haven't tried it with SuperHQ on, if that fixes the issue I'll be using this emulator exclusively from now on. Stretching works perfectly for the video, and it is very convenient to not have to change video settings to play SMS games.
SuperHQ won't fix it. The beep is present in Fusion though its very low. You'll have to hear closely.
And oh, thanks for the nice comments 

 .