Bizarre problem - Tivo or Cablecard?

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Noticed several duplicate channels listed in my guide this evening (not like 301 and 416 for HBOHD, like 301 HBOHD and 301 HBOHD). Thinking this was just a glitch like had happened before (with the WEDU-PBS DT 'side' channels having double listings 201/201 and 202/202), I went into the settings and deleted the duplicates so as to clean up my guide.
Then the fun started. I had called Comcast about a billing issue and then turned on the tv. Noticed I was missing some channels, weird ones to be missing (several HD channels, some TMC channels), and the missing channels would change as I went up and down !!! Fearing a(nother) cablecard glitch, I called Comcast back, and was assured that indeed the cable cards were properly programmed.
At this point, I rebooted the TiVo. When the Tivo came back up, I waited for 'acquiring channels' and then went to Starz HD (one of the channels which would not come in), it came right up. I then noticed in the guide that there were two 417 STARZHD channels, along with several other channels being duplicated. The channels showing up duplicated were those that would not come in before the reboot. My concern then became bewillderment as the duplicate channels disappeared from the guide listing!!
Now I appear to have all my channels, and my guide is back to normal, but Whiskey Tango Foxtrot...

Also, why do I have to go back into settings...channels... to uncheck HBOLAT and HBOLATP (among a few others) every time I reboot? I have other channels unchecked and they don't come back checked after a reboot...