I am aware that this has been posted a ridiculous amount of times, so I'm not going to whine. Keep up the great work, starting a free community project is never easy. Especially one this size.
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Windows 7 x64, -
English F:3 / F:NV -
Check my other specs on the profile page
Anyway, I have a TaleOfTwoWastelands.bsa patching error. I did notice something slightly odd about launched parameters and could explain the issues you have been having regarding folders/different partitions.
Pay particular notice to the directory parameters. I'm not going to pretend that I know I/O operations well (because I don't) and have only done a bit of I/O programming, but the paths are strange. Note the use of "C:\Fallout3\\Data\..." and "C:\\TempInstall". I have only noticed a double slash with partition roots (e.g. C:\\) so the first path parameter seems malformed - especially since the root (C:\) has only one slash, and "Data" has only one as well.
I haven't looked at BSAopt.exe 's documentation or anything, but I just feel that this is important.
I will try the install on Windows XP, see if I have any luck with that. I had the same errors regardless of the location (Desktop, proper Steam directory, root of C:\)
Hope this helps somehow,
SS