Just for reference, and to add my own experience as a FLAC user, I have
never once had FLAC skip on either of my primary listening platforms. The CPU/memory stats of my systems are as follows:
1 - PC: P4m 2.0GHz, 512MB RAM
2 - Kenwood Music Keg: 74MHz ARM processor, 32MB RAM
If FLAC playback is skipping on a PC even fairly slow by modern standards, it would seem that something else would be affecting it, like perhaps fragmentation as previously mentioned. (Because no modern PC is as limited in CPU and memory as my Music Keg, and
it does fine.) However, as Doctor stated, fragmentation is usually more of an issue with FAT than NTFS...and in my experience it's not much of an issue with FAT32 as well because I have never defragged my PhatNoise DMS (cartridge for the Music Keg with FAT32 formatting), and even after switching out music files on it for a year or so, FLAC playback has still never skipped.
Vorbis playback with limited overhead is another matter...
@dewey1973: As for eliminating FLAC skipping, if you're using FAT disk partitions, then disk defragmentation would be my first recommendation as well (looks like you're already trying this). If it's FAT32 or NTFS, then perhaps Norton "Disk Optimization" may make a difference (similar to defragmentation). If that doesn't work, and I know the "f" word is usually only a last resort, but formatting the disk with larger block sizes (perhaps 32K) would improve audio file playback performance. Doing this on my DMS cartridge slightly improved Vorbis playback on my Music Keg which was having skipping problems with higher bitstreams, as in >180kbps. Don't ask me how it could (even before reformatting) cleanly playback 800kbps FLAC bitstreams. Lower decoder memory requirements, perhaps?
Anyway, if you have an "extra" HDD lying around, then testing the larger blocksize approach for helping FLAC playback may be worth a try.
Edit: As for *.APE and *.LA formats, I haven't tried them, so I couldn't speak as to performance problems they may run into. I've heard, I believe, that FLAC has lower system overhead requirements than most other lossless codecs for clean (skip-free) playback.