Sorry, my explanation about Tapper was incomplete. The problem isn't the interlaced screen (480i) per se. The problem is that the programmer apparently attempted to make it interlaced but left some incorrect timings. This is the explanation posted by alex_79 in Atari Age forums in 2013:
BTW after looking more closely, the original NTSC version of Tapper seems to purposely enable and disable VSYNC on cycle 41 every other frame. Storing to VSYNC register takes 3 cycles, so the operation starts at cycle 38 which is exactly in the middle of a scanline. This could indicate that the programmer intention was to generate an interlaced signal, albeit the scanline count was wrong and the resulting "fields" had 261.5 scanlines each instead of 262.5 which should be the NTSC standard.
https://atariage.com/forums/topic/19345 ... try2872128
I don't remember any issues with Turmoil on the original hardware, even with 2600RGB + Framemeister/OSSC. I just tried it on MiSTer and it flickers when VBlank Regeneration is on, but works fine when this option is off. This is with the HDMI output.
There was a standard to be followed regarding the usage of VBlank and VSync in Atari 2600 games, as described in the Stella Programmer's Guide, so the game would work on any TV set, according to Atari research. But the programmers would often not follow the standard, either intentionally or unintentionally. CRTs were often forgiven about this, though I remember some poorly programmed games (like Condor Attack) failing even on CRTs (rolling image sometimes). Modern TVs don't like all those non-standard signals, though I don't know the exactly issues with PVMs, since they are still CRTs after all.
Now we basically have two paths: trying to fix each game that is out of the standard or adapting the Atari 2600 core to handle these issues in the best possible way. Either way I don't have the knowledge to handle these tasks. But I believe the second one is preferable, if possible.
As far as I know, Turmoil doesn't have a fixed version.