When files don't show up in the Mac OS finder

... then it's likely that the files have the "hidden" attribute set.
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