I've been running Unitrunker on the Metrolinx system for about a week and have not seen a single encrypted transmission.
What I have found is that most users are using the TDMA mode (Phase 2), however for the time being, most of the Train talkgroups are still using Phase 1.
GO Enforcement as well as TTR are on Phase 2. I suspect it is just a matter of getting everyone switched over, then it'll all be Phase 2.
I suspect that's why radios are showing encryption - it tunes to the voice channel and doesn't get decodable P25 traffic, so the scanner thinks it is encrypted. Dunno for sure though.