I'd have to agree with Whiskey3JMC and tvengr about the squelch setting.
If you have it set to low, lower than 2, you might notice a slower scan time. I do on my conventional systems set up.
I just happened to have turned the squelch knob one time instead of the volume button, not really paying much attention, and the next day I noticed my scanner was considerably slower.
After doing some Google searches as to what might be the problem, I came across a RadioReference thread and someone mentioned the squelch setting being to low. I checked mine on my BCD996P2 scanner and sure enough it was set to 1 or 2 (I don't quite remember). As soon as I put it on 4, the scanner was scanning at its normal scan speed.