In theory, using the same playback chain (i.e. same software player, PC, speakers etc.) that's not possible. FLAC is designed to be bit-for-bit identical to whatever WAV file it came from and you should be able to convert back and forth between the two formats infinitely and see no actual change in the data that is output. If this is not true for you, I would think there might be something wrong with something in the chain, be it the encoder, the player etc.
Some arguments can be made that the CPU overhead required to decompress FLAC might introduce some jitter to the equation, but most tests that I've seen peg this number at less than .2% of a modern CPU, while this number is actually often
higher for WAV. Other than that, you might be able to make an argument for bit rot on magnetic storage, but that's about it.
All-in-all I'd be incredibly surprised if you could tell a difference between FLAC and WAV with consistency/reliability under blind listening conditions. and I would be absolutely mind blown if you could tell a difference between two FLAC files encoded with a different encoder.
I must admit that all the conversation on this board about hearing differences does make me wonder just how damaged my hearing is