XXHighEnd

In order to eliminate perceived differences between FLAC to be converted to WAV and native WAV, two explicit options are available (beyond version 0.9z-6) :

Don't start Playback at all

This is an option in Settings meant to be used together with Unattended Playback with the objective of letting all come to rest in the PC after FLAC to WAV conversion has taken place;
When perceivedly all has come to rest and the whole PC is set for playback start (which is an automated process by itself), after Play has been used earlier on (screen went blank etc.), Alt-p can be used to start Playback for real.

Playback Drive/Folder

An optinally to be filled in Path in Settings can appoint this Drive/Folder, and special further treatment by XXHighEnd should eliminate any difference without the sort of hussle from the above mentioned option (if that option helps at all).
Its working is similar to the Copy to XX Drive setting (in Settings) but that option does not treat all situations equally. The Playback Drive/Folder tries to 100% accomplish that all is dealt with in the same fashion.