Ok, well, the issues you had occurred for two reasons.

1) The patch was zipped, and the auto-extractor doesn't make it clear exactly what it's going to do, because it isn't really designed for housing executable files, but rather for containing a directory for extraction in the case of programs which don't need to be installed per se

2) You also unpacked the game files, which you dont' need to do, and that was the cause of the delay - the patch itself took me about 20 seconds to install. The unpacker is simply a batch file which works through the command line, and that's why a cmd window popped up (it's also why you had to copy it to the m2tw directory, as it contains a relative rather than an absolute path to cater for people with varying install directories)