Well setting the settings as advised earlier, and schedualing the service to start in the morning hours worked for us... At first.
Universal search was working again.
After updating to 2012 SP1 HF3 however, the indices (which were on a second SSD) seem to have disappeared. No new indices are being made, and the Universal search is, again, broken. We didn't change anything to the config file after the update, nor did the update itself seem to change anything. Settings are exactly the same as before.
In my honest opinion, it's time that Sage gets it's "Act" together and cleans up the problems surrounding Sage Act. Be it with the program itself, or the e-mail client.