ilrosewood, I have the WinTV-DCR-2650 on Cox (Omaha). sitlet is correct - when my CableCard was activated, I had to ask the tech to do a "cold hit" twice - the second "cold hit" finally got it up and running.
As for the "analog channels" - the WinTV-DCR-2650 does not have a built-in NTSC tuner, so it won't be able to tune in any of the channels that you'd get just by plugging an old NTSC-only TV, VCR, etc. directly into the cable jack.
In Omaha, Cox does simulcast these same channels in digital SD, and if you're using a Cox DVR or receiver, you're actually tuning the digital SD feed of those channels. However, if you are using a CableCard device, it appears that Cox does not send the channel information for these digital SD channels to the CableCard - when I look at the channel lineup information in the Hauppauge menu, it does not contain any information for channels 2, 3, or 5 through 70, all of which are broadcast in analog as well as digital SD in Omaha. I suspect that if Cox isn't supplying this information here, it probably isn't in its other markets either.
I already had a NTSC/ATSC/ClearQAM tuner card, so the fix for me was simple enough - just use that card to tune the few channels that are not sent in either digital SD or HD, and customize my channel lineup in Windows Media Center with the HD channels being the default.