Please! Change the priority

[Selur]

then why do they work? HandBrake, Shutter Encoder and StaxRip

only one that is similar to Hybrid is StaxRip the other two don't use Avisynth or Vapoursynth. Also Handbrake and ShutterEncoder use the libraries not the command line encoders.

I wrote multiple possible issues, which you did give no feedback.
You didn't even report whether using a higher priority fixes the issue for you but expect that I spend time writing code for you.

If you won't give understandable feedback don't expect me to write code.
If you are not able to prodive understandable feedback to questions, best stick with tools that work for you. Since Handbrake, Shutter Encoder and StaxRip work for you, you should be fine.

Cu Selur

Ps.: btw. one also can change the default priority that Hybrid starts processes with by setting:

[General]
niceness=XXX

in the misc.ini file (see hidden options thread)
allowed values are:
0 <> NORMAL_PRIORITY_CLASS
19 <> ABOVE_NORMAL_PRIORITY_CLASS);
49 <> HIGH_PRIORITY_CLASS
99 <> REALTIME_PRIORITY_CLASS