First, the reason you are hearing garbled transmissions is because the NJICS uses linear simulcast modulation or "LSM." There are several threads in the Uniden Forums that explain why today's scanners are having a difficult time demodulating the audio. The basic concept is you are receiving a signal from two sites at different times, causing garbled, inaudible or missed transmissions. The NJICS system is also a Phase II system, meaning it uses TDMA vs FDMA. Newark Fire runs TDMA and I've also noticed the scanner having a more difficult time compared to lets say Fairfield PD, who is running FDMA. If I have my scanner in the same spot, I'll hear Fairfield clear as the day while Newark is all garbled. If you again go to the Uniden forums, you will see countless posts of complaints. It's not a GRE/Whister vs. Uniden one is better than the other either as I get the same results regardless of brand used. Until a scanner manufacturer decides to spend the $$$ on proper HARDWARE (not firmware update), you'll never get the type of audio quality you would compared to an XTL5000 or APX for that matter.
As far as scanning all available sites and locking on one, I will say that is not a good idea for this system. Certain traffic is carried over certain sites and not on other sites. So, if you are locked on to Randolph, you wont hear Newark Fire which primarily uses the West Orange Simulcast (unless a Newark FD radio affiliates to Randolph). This is why sometimes you'll see posts of activity on a certain site that comes and goes. For example, a poster heard Newark Fire on the Bordentown site which is unusual. However, that was the day that Newark had a 2 alarm structure fire so I'm sure it was an off-duty who lived down there turning on his portable and listening in. Try programming West Orange as a standalon system if you can hear it from your location.