Greetings daniels,
I'm afraid to tell you that all your problems are probably related to the way you upgraded it...
The first thing the doc tells you is:
IMPORTANT: Upgrading from 3.1 to 3.1.1 and from 3.1.X to 3.2 need specifics steps described in two section below
I don't know if you did this or if you upgraded directly from 3.1 to 3.2.1... let's hope not. :)
In any case, if you followed these steps correctly...
Have you upgraded from 3.1.X to 3.2 and from 3.2 to 3.2.1? or from 3.1.X to 3.2.1 directly? :P
The first choice is the right one... Otherwise this would explain your problems.
If even still you upgraded everything correctly...
Then this problem is worth a jigsaw. :P
Regarding the problem about the tar gz... you are right, and will change it ASAP. :)
Regards.