As already stated, Unitrunker will decode FDMA control channels, which 99% of TDMA systems use. And just so that you're clear on the terminology, as one of your previous posts had you sounding a bit confused: FDMA = P25 Phase I, TDMA = P25 Phase II. The South Dakota system appears to be TDMA capable, however thus far all of the talkgroups are flagged as FDMA in the database.
Make sure you have the system setup as APCOP25 in Unitrunker, not Motorola. It sounds as if you never changed the system type when they stopped using the SmartZone system, which would cause the software to not properly decode the control channel. The new system is a true P25 system, the old system used P25 modulation for voice traffic, but was not a true P25 system.