I'm not in the San Diego area, so I don't know if this post will help, but...
Have you gone through the manual add for all of the digital stations? (If you have, ignore the rest of this post.) For example, I have a station that is carried across digital channel 62.3 but reassigns itself (via information sent on its signal) to channel 42.1. I also have stations for which the 4200A counts as having a signal, and with positioning I can sometimes pick up a lock, but will not show up on auto add.
Have you gone through the manual add for all of the digital stations? (If you have, ignore the rest of this post.) For example, I have a station that is carried across digital channel 62.3 but reassigns itself (via information sent on its signal) to channel 42.1. I also have stations for which the 4200A counts as having a signal, and with positioning I can sometimes pick up a lock, but will not show up on auto add.