File info greyed out & peculiar finder behavior.

A while ago I went into Terminal to 'show hidden files' in order to show '...And God Created Woman.mpg' which disappeared (because of the leading dots), I didn't mind the invisible files at first but when I tried to drag and drop copy my Music folder to back it up it copied maybe 20% before saying 'Cannot replace .Dstore' or something like that and wouldn't finish the copy. I tried the reverse of what the article on showing hidden files said thinking maybe that was the problem but no matter how I tried I couldn't get the hidden files to hide again. Now I'm having trouble moving files to an external drive at all, it tells me I need to authenticate but doesn't give me that option, and all the file info is half greyed and my library is completely greyed. I'm thinking I screwed something up in Terminal but not sure what. Also, there isn't a recent enough backup of the system to simply restore. Here's a screenshot:

I tend to use Terminal to handle invisible files & folders, so I don't use this option generally.
The same behavior in every user suggests the preference is either system wide or you may have set a flag on the HD? Do you use Xcode?
What happens if you check the 'global' domain…
defaults read -g com.apple.finder AppleShowAllFiles
defaults read -g com.apple.Finder AppleShowAllFiles
These don't exist for me. You can write the to default the same way as before, but it needs the '-g' flag
Does your Terminal history still have the old commands? Enter this in Terminal & hit return…
history
then search (via cmd+f) for the 'defaults' commands etc. You may have done a different ommand around the same time.
I'll try to see what otherways the visibility can be set.

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