Comment 14 for bug 1948882

I have switched to the flatpak version as @del00m proposed and indeed it starts correctly. That version of PulseEffects is 4.8.5 while the repository's is 4.8.4.

Changelog for 4.8.5 just says "Improved compatibility with dconf 0.40. Now our plugins should be enabled when using this version.", so maybe the solution is to update the PulseEffects package in the repository to 4.8.5+ :)