Lots of probabilities. Like trentbob said, auto filters will s l o w things down considerably... especially if you accidently set the global to auto. Also, check your digital waiting times and delays.
And sites: Remember that EACH trunking site, the radio 'listens' to it to see if there is any grant requests, then moves on to the next site. It does this for EACH site, so the more sites, the longer it's gonna take. Either use tighter location control, or avoid those sites out of range, or you don't want/need to monitor.