Couple of things to check and to know:
-The Pro96 scanner has a few issues: It has problems "motorboating" before digital transmissions. It can get annoying. Sometimes it just motorboats and doesn't decode digital transmissions at all. Also, as you mentioned it does suffer from some front end overload and simulcast distortion. Change your location, try different antennas, etc.
-Make sure you've programmed in the CMARC system - Harford County Simulcast Site. AFAIK, the Baltimore/AA and Howard/Carroll sites do not broadcast the Harford County talkgroups. (I could be wrong on this).
-You may want to double check the Pro96 specs (
Pro-96 - The RadioReference Wiki) ... it does not officially support the 700mhz band. I think it starts at 806 Mhz, BUT I believe it will allow you to program them in. The Harford County CMARC site includes multiple 700Mhz band frequencies and uses them for control channels. Just remember that the radio might accept the frequencies via programming, but may not receive well on them (IIRC).
-The Pro96 only decodes APCO P25 Type 1 systems...but you should be okay there for now.
-Check you're on the latest firmware, etc. I believe the wiki link above references that and provides a download link if you need them. Not sure if they're still available, though.
-If you're receiving all the TG's you wish to monitor on the Balto Co/City systems, etc...it sounds like your programming is probably good, but best to double check what's in the scanner, plus what I've mentioned.
-Note: I own a Pro-2096, and possibly still might own a Pro-96. They're the same radio inside, just one's handheld and one's mobile/base. I just haven't actually used them in a looong time. If I were to use them again, it would be for listening to anything that's not digital or digital trunked systems.
-I still have the programming sw for these radios if you feel the need to upload your programming file, I could take a look if you're still stuck.