Ok, I tried out Captain Fizz on Steem...

Here's the deal - the intro runs at the right speed and no flickers there, but on my MSTE (regardless of 50hz/60hz) it is running insanely fast.  The waving text and music are moving and playing at incredibly the wrong speed.  Like it's at 16Mhz from the start.  And the game is playing way too fast as well, like it's always 16Mhz.  As a matter of fact it plays at the same speed whether you choose 16Mhz or not from the intro.  

This is the issue with many of the games that I posted as 'running fast'  I know the difference between 50hz/60hz timings, but this is way too huge of a difference to be that.

EDIT: I just verified Captain Fizz behaves correctly (the same as STeem) on my 1040ST.  No flickers, sane music and correct game speed at 8Mhz.

The only conclusion I'm left with is that the games exhibiting the incorrect behavior are simply running at 16Mhz from the moment the menus start on the MSTE.