Here is an interesting update. I spoke with Apple Care and they of course had no idea there was any problem, but the nice girl suggested I reinstall El Capitan just in case there was some corrupt part of the install. So, i downloaded a fresh version and reinstalled to find out there was not a single change to my issue. The scheduled call back from Apple Care with another guy, also had him baffled. I told him the Snow Leopard disc worked fine when I was reinstalling the OS after the hard drive replacement. The two different discs, actually, 3 discs I tried were all Microsoft related, Office for Mac 2011 and Windows 7 for installing on VMWare. Well, I decide to jam the Snow Leopard disc in for grins and shazam, it works! Then I grab a dvd movie, Catch Me if you Can and it works too! It turns out that El Capitan is apparently allergic to my Microsoft discs... go figure. So, now I am downloading versions that I need to install off of a USB flash drive...
So, it is apparently related to the El Capitan update, but seems only affected, at least in my case by MS software.