I have heard simulcast distortion on other frequencies (most notably 154.415 in Albany County), so I know what to listen for. I heard none on 800 MHz.
That's analog simulcast. How about P25 simulcast? It will cause serious hits in the decode rate due to intersymbol interference which will affect both the audio and also the control channel decode. No "warbling or whining", just undecoded or extremely distorted audio and loss of control channel sync.
We have confirmed that there are at least 2 control channels active in this system with different site IDs, the one you heard and the one on 852.6 MHz that Warthog1 hears (not "everyone" is hearing only 1 as you state), which is licensed at Fraker (Edinburg) and Lakeview. We know Warthog1 is near Fraker and probably hearing that site since he states Lakeview is not built yet. That implies a multizone system. Quick look at the frequencies in the RR database shows a 3rd set at Lake Luzerne and Hadley, so there may be a 3rd zone yet to be discovered or on the air.
(Warthog1, do you show any neighbors besides T0101 in Unitrunker?)
The fact that all of the same frequencies are licensed at Corinth, Wilton, Saratoga Springs, Ballston Spa, Barkersville, Stillwater, Halfmoon 1 and 2 implies those sites are or will be simulcast. Given the number of channels, it is unlikely each one of those sites could be it's own zone as each would require it's own control channel and a huge duplication in working channel traffic as those would be very small and overlapping zones.
I have heard units on the 911 channel, who are coming though the 800 system (i.e. sheriff units, no repeater tail), scattered around the county. Seems unlikely they could be operating on Bakersville 800 from all of those areas. In fact, if EMS is operating countywide on the 800 system, then it's highly unlikely that Barkersville could be providing that coverage.
Stepping back from the technical, why would they move users from a multisite VHF system to a single-site 800 system that wasn't finished, when we know the VHF (e.g. 911) is still working (since the NYSP are still using it - have a repeater tail), and then move EMS and plan a near move of fire.
I still think it's very possible we are facing a hard to scan system (at least in the south and east high site density areas), especially given the number of sites and the probable overlapping covearge as a result. These systems are designed for commercial P25 radios with high quality receivers that are designed to work in a simulcast environment with LSM (versus plain C4FM in a regular P25 system). If you search the forums here, you'll see this is a common problem with certain P25 simulcast systems. Some scanners are better than others. Some systems work betters than others. Sometimes it can be mitigated through the use of directional antennas (high gain narrow beamwidth Yagis) aimed at, or sometimes away from, a certain site.