Sounds trivial really, but it did leave me stomped a bit today. Files showed up fine in the terminal when I copied them, and also Forklift showed them (turns out it only did because I had it set to also show hidden files). Anyway, finder of course didn't show the files at all.
To remove the hidden attribute, type:
chflags -R nohidden <files>
to check which extended attributes are set:
ls -lO
