The root cause is SNES (clone) and for genuine one a solution (de-jitter mod) has been available for many years. A SNES core with digital output ends up constantly re-triggering frame syncing on Pro (properly enforced on upcoming fw) since its framelock is designed to operate with constant number of VCLKs per frame (that you get from any normal HDMI source or from digitized RGB). Aside from turning framelock off, there are essentially 2 other ways to solve the problem:
* addition of de-jitter option on the SNES core (which could also improve compatibility with some picky CRTs)
* re-implementing Pro’s framelock via general genlock which adjusts timing based on source vsync alone
The latter might also have some other minor benefits on Pro, but it’s currently not high priority since the existing solution works well with vast majority of sources.