Blindjim,
I do find still greater diffs using FLAC vs. Apple lossless too... and this might be due to the media player or codec (s) being used. FLAC having simply more resolution and detail which offers greater presence. AIF is quite close though... and actually a near toss up.... again, I'm thinking it's the decoders and encoders being used.
I'd like to point out for the sake of clarity that you are experiencing some kind of placebo effect here. It is mathematically impossible that FLAC, Apple Lossless, and AIFF or WAV are producing difference results in sound quality.
They are all going to produce exactly the exact same bits when decoded, and they'll do so repeatedly without error. It's what makes them lossless.
It's precisely the same thing that makes an archive that's been zipped, gzipped, rar'd, or bzip2'd produce exactly the same uncompressed result when it's been expanded/inflated. The compression/decompression mechanism is lossless.