Reggie,
I've gone through a couple of notes, and when you tune a channel on the Prime, it unencrypts that particular program on the mux. So, by tuning with the vchannel, the Prime is essentially tuning the mux, selecting the proper program, unencrypting it with the CableCARD, and then passing that filtered stream through as if it were unencrypted.
To see whether any of your channels are truly unencrypted, run a scan through the hdhomerun_config app:
hdhomerun_config FFFFFFFF scan /tuner0 scan.log
Then browse through the resulting file to see if any of the muxes actually contain unencrypted programs.
EDIT:
I just ran a quick test on my end, and this is what I get:
$ hdhomerun_config FFFFFFFF set /tuner0/vchannel 702
$ hdhomerun_config FFFFFFFF get /tuner0/vstatus
vch=702 name=CBSHD auth=subscribed cci=none
$ hdhomerun_config FFFFFFFF get /tuner0/status
ch=qam:145750000 lock=qam256 ss=100 snq=100 seq=100 bps=9090176 pps=0
$ hdhomerun_config FFFFFFFF get /tuner0/streaminfo
411: 0 (encrypted)
412: 0
413: 0 (encrypted)
414: 0 (encrypted)
415: 0 (encrypted)
tsid=0x16FE
$ hdhomerun_config FFFFFFFF set /tuner0/vchannel none
$ hdhomerun_config FFFFFFFF set /tuner0/channel qam:145750000
$ hdhomerun_config FFFFFFFF get /tuner0/streaminfo
411: 0 (encrypted)
412: 0 (encrypted)
413: 0 (encrypted)
414: 0 (encrypted)
415: 0 (encrypted)
tsid=0x16FE
$ hdhomerun_config FFFFFFFF set /tuner0/program 412
$ hdhomerun_config FFFFFFFF get /tuner0/streaminfo
411: 0 (encrypted)
412: 0
413: 0 (encrypted)
414: 0 (encrypted)
415: 0 (encrypted)
tsid=0x16FE
$ hdhomerun_config FFFFFFFF get /tuner0/status
ch=qam:145750000 lock=qam256 ss=100 snq=100 seq=100 bps=8226880 pps=0
$ hdhomerun_config FFFFFFFF get /tuner0/vstatus
vch=0 name= auth=subscribed cci=none
$ hdhomerun_config FFFFFFFF set /tuner0/channel none
As you can see, when tuning by vchannel, the mux is tuned and a specific program pre-selected/filtered, and its encryption removed. However, when manually tuning by specifying a particular frequency/mux and then manually selecting the program to filter, it is still reported as unencrypted; the difference here is the vstatus does not display the program information on the channel as it does when tuning via vchannel.
In the past I asked over at the SD forums about receiving the full mux and selectively unencrypting multiple programs, and as told it was not possible. Because of the way that decryption with the CableCARD works, the tuner (and therefore full mux/frequency) will be filtered to only display one program.
In short, the channels you are having issues with are not truly unencrypted, but rather reported as such because the Prime is handling the decryption through the CableCARD and passing out an unencrypted stream.