I am experiencing this also, pre and post transition for CJMT-DT, and using a HDHomerun tuner. After debugging the stream, the guys at Silicon Dust say it is a config issue at CJMT-DT whereby WMC does not like it and does not display the stream. VLC will play it, however. Si Dust was supposed to notify CJMT-DT, but I have not heard anything yet.
The only change that matters is setting it to Other: ATSC/QAM.
The station encodes their signal in a way that puts the clock reference separate from the video, which is technically valid, but extremely uncommon. WMC's channel parsing code does not handle this correctly, and will not request that the HDHomeRun send it the clock when tuning the channel. The clock is used when decoding the video, and so WMC will just show a black screen if it isn't there. The Other: ATSC/QAM setting causes the HDHomeRun to ignore what WMC is requesting, and just send the full unfiltered stream.
We attempted to contact the station regarding the issue multiple times, and they never responded.
There is extra details there if you have problems with WMC guide linking the new Virtual 40.1 with Channel 40, my system was still assigning Virtual 40.1 to the old channel 51. I had to manually add it to setup the new channel 40 and link the guide data to have a fully working channel/guide.