Assuming you used tar, it sounds like you've just copied a new OS on top of the old one - if you had used rsync it would have deleted any files from the target which didn't exist in the new OS (which in your case would be mostly application-specific files).

Chances are the apps you installed for the old OS (which were on the MMC) are still there as these are new files and links that don't exist in the new OS.

What you ended up with on MMC is a merger of 2.2006.51-6 + apps and 3.2007.10-7, with the latter replacing any existing files provided by 2.2006.51-6 yet keeping all the new application files... it's probably understandable that it worked, though I'm not sure I'd call it ideal!