On upgrade from 4.5.8 to 4.6.2 CiviCRM menu disappears until scroll, then scrambled
I was able to finally figure this out (not why, but how to fix). It somehow had to do with the Zen sub-theme I was had created was not playing nice with version of CiviCRM past, I think, 4.5.8.

I downloaded another version of the Zen 7.x5.5 version sub-theme and re-built my theme and was able to upgrade successfully. Thank you, Michael, for leading me down the right path.