You both have programming issues. Either talk group programming or something else. All scanners that could trunk the "old system" can scan the "new system" just fine.
For starters, if you don't have the Control Channel Only feature, you have to have all the freqs programmed.
( site 001 )
866.0500
866.2500
866.4000
866.5875
866.7125
866.7750
867.0500
867.1250
867.3125
867.3750
867.4625
867.6500
867.8125
867.8750
867.9000
868.1125
868.1875
868.2625
868.3375
868.5750
868.6375
868.6625
868.6250
868.9000
( site 002 )
866.1125
866.1375
866.3500
866.3750
866.4375
866.6375
866.7500
866.8125
866.8375
867.1000
867.1625
867.3500
867.4125
867.4375
867.6250
867.6875
867.8375
867.9375
868.1375
868.2375
868.2875
868.4375
868.5375
868.6125
868.6375
868.7375
868.9375
Because the Talk Groups can appear on either site 001 or site 002, you will need to have duplicate talk groups for each site.
For example
Elk Grove PD Ch.1 TGID = 52432
Normally this talk group shows up on Site 001, but it can show up on site 002 depending where the transmission is coming from geographically. So, you will need to also program talk group 52432 into Site 002.
If you don't have the contral channel (data channel) programmed, it's not going to work.
Since the "change" there are only two big differences.
1. New talk group IDs
2. Talk Group IDs are not exclusive to just one site, they can appear on both sites.
This thread listed below explains a lot about the "new system"
http://radioreference.com/forums/showthread.php?t=35476