This in my opinion is a major shortcoming of all current scanners.
I found out how big of an issue this is after a neighboring county started migrating to a mixed-mode P25 system. Although currently there are very few P25 transmissions, eventually most operations will be P25, while paging and interop will be analog.
There is no good way to program this system in my Uniden or GRE scanners. If I program it with no tone or NAC, I get interference from distant stations on the same freq. However if I create two channels, the scanners "hang" on the analog channel when there is a P25 transmission and vice versa, resulting in large delays before the audio unmutes. The latter method also prevents assigning this system priority. I can only imagine how annoying this will be when they start using P25 more often.
Now, every P25 radio made (be it Motorola, Kenwood etc.) has had mixed-mode capability from the start. That means ONE channel, with CTCSS/DCS for the analog side, NAC for the digital side, and it automatically switches mode depending on the type of incoming transmission.
Why has the scanner manufacturers not taken notice of this seemingly essential feature that every professional radio has? I can not imagine mixed-mode systems being very uncommon, and as more rural areas go P25, possibly operating like my neighboring county, I see this becoming more of an issue.
On the subject of P25 annoyances on scanners: Why can Uniden not display radio ID's on P25 conventional channels without creating a stupid P25 "One-freq-trunk" system? Once again, every P25 radio made (with a display) effortlessly displays radio ID's right there on that one mixed-mode channel. I believe the new PSR-800 does this also, not sure about the HomePatrol.