FLStudio 12.3, and I have found that it does not save my settings at all. In all my other DAWs (Pro Tools 10/11/12, Cakewalk Sonar Pro, Cubase 8.3 Pro, and Studio One 3 Pro) this is not an issue ...
Thought it was a bug with the WaveShell at first but Auto-tune EFX 3 (which is only offered in VST3 format) also reverts back to its default state when re-opening a project.
macOS Sierra 10.12.5
FLStudio Beta Candidate 1.41 ...