I'd start by figuring out which of the 4 copy files check boxes it is having the issues. IIRC they are Launcher files, portal.dat, cell.dat and Misc Files. I'd then copy whichever file that NOT having issues and then let the launcher patch whichever one files that *DO* have issues.
In other words you DON'T have to use dual client to copy everything from the base install directory, I've forgotten to copy stuff over some patches and it works, and other times used files from a 'extra' install to back fill corrupt files in working directories (memo to self, it's time to copy the files into my extra install again). I try to maintain one more install directory then I am using simultainious clients, it has prevented me from to run 2 clients from the same install directory, *THAT* really screws the files up(not that such has happened recently, but I have had happen before in the now distant past).... HD space is cheap enough that it's not a big deal to me to devote a bit more space to AC. It also works a same area 'back-up' if say the launcher screws a file up.... It's happened before to me, and it saved me a number of big DL's....
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/a Devil's Saint says, "what we teach our Children we become" June 3, 2008