I could speculate on the reasons, but the problem seems to lie in the fact that we are at a higher elevation than the transmitter antennas and that is causing strange problems. Moving the antennas might fix the "problem of the moment" but the new location will likely be bad under slightly different conditions. I've had my antennas in 3 different locations and all the stations act differently in different locations. There is no magic spot in our situation.
Roy - Honestly, 99% reception is pretty good in your situation. That's about what I say I have here. Can you switch to the SF stations when there is a problem? That's what my friend does up there. The SF stations are not useable here but I can get NBC and ABC on KSBW essentially 100% and FOX on KCBA 99%. CBS is the only major network that I don't have a reliable back-up for. KION is too weak and has co-channel problems with KEMO. PBS is virtually 100% with KVIE.
Somehow I missed it along the way. What antenna did you split into 2 parts? I see you talk about the Clearstream 2 but what about VHF? Personally I think the 91XG is much better than the Clearstream 2.