Acrobat 6 pro was what.... 2003?
You're talking about seven-year-old software, which is an a lot of cases unable to open PDFs created now unless they were intentionally made compatible that far back.
Chances are that reader 9 updated some core files that rendered Acrobat 6 unusable. It's too far back to "upgrade" (7 was the cutoff for that I believe) so either reinstalling from the original media (the OEM disc that came with your system, if it had Acrobat 6 on it) or purchasing Acrobat 9 Pro are your options.
A side note, if your system came with Acrobat 6 installed, it's probably time to look at a newer, more up to date system as well.
It isn't recommended nor supported to have both Acrobat and Reader on the same Windows machine.
You likely broke your version of Acrobat, If it came installed on your machine, you may have to restore it somehow (sometimes they come with a partition that holds your software. Sometimes not).
I'd add to that "it isn't recommended to have Reader and Acrobat together on a Windows machine." I've done it on Mac for years and have never had a problem.
Correct. Mac doesn't have this issue.