I'm just now digging into the details of setting up HLSL. Still learning, but one important thing that I learned recently is that PREscale is scaling that is done by the cpu before it is sent to the graphics card. So raising the prescale makes a lot more work for the processor, not the gpu.
Most of the classics ran fine on my system with the prescale set really high (which makes it sharper), but Popeye, Galaga, & Frogger slowed to a crawl.
I looked them up and it turns out that they all have discrete audio filters emulated which makes them more demanding on the processor than other games from the same era.
Not sure what your prescale is set to now, but lower it until the game runs at 100%.
If it's already at 0, then you just don't have enough oomph to run hlsl on those games.
You can make an individual ini file for those particular gameswith hlsl turned off.
(or make the individual ini files with a lower prescale, so other games are still sharp)
That way you can still have it in other games.
EDIT: to further elaborate, say the original game ran at 320x240 and you are running your monitor at 640x480.
There is no point in having prescale set to anymore than 2. Likewise for higher resolutions.
No point in scaling it larger than your monitor can display.