Given a sufficiently crappy hardware setup that the CPU activity is injecting noise into the audio path, then in principle the FLAC decoding could be more inconsistent in that regard, because the processing is much more data-dependent with FLAC. But even with WAV your CPU activity is not going to be completely regular, so this still stretching credibility as something you should actually care about instead of just fixing the underlying problem, which should only be a problem on utterly bargain basement non-audiophile/fool setups anyway.