If I'm correct and those short freezes are due to the memory/thread handling in Avisynth.
Try:
1. enabling Filtering->Avisynth->Misc->Script->Miscellaneous->Disable MT
This should slow things down, but also remove those freezes.
2. if the above helps, disable it and try using a lower MT-thread than you effectively use in your Avisynth script atm. (start with 2)
Another 'workaround' I found is increasing the memory max for Avisynth scripts (assuming you got enough free ram), more than Hybrid supports atm.
=> I'm uploading a new dev (should be up in ~10min => it's up), assuming you have enough RAM (and use 64bit Avisynth), you can now instead of lowering the MT count, increase the 'Memory max' for example to 16384, this should help with the occasional freezing. (at least it does here)
Cu Selur
Ps.: In general, I would recommend switching to Vapoursynth.