Except that you best go for upgrading to 3.2.1 I canTt tell you much with certainty.
Regarding the slow start, Joe Clarke said a while ago the windows doesn't always wait long enough for LMS to shutdow the db's. I guess this causes slow startup as it ries to fix stuff at boot up. So maybe it is better to do a manual net stop crmdmgtd if you know the box has to reboot.
I would try to get another server and try to rebuild the server most impacted now. (no guarenties)
- keep the same hostname as the most impacted machine.
- Install lms 3.2 with minimal config.
- upgrade to lms 3.2.1.
- make a backup of the clean system to fall back on.
- restore a backup of the most impacted machine.
You can change ip address when the lms services are stopped and take on the ip of the prod machine.
If your servers are in a cluster then you need to read up on that before you give the new machine a production address.
Cheers,
Michel