I finally got the quicktime working but it was a very long trial and error process. Installed 10.6, then upgraded to El Capitan, but no good. Installed 10.7.5 then upgraded to El Capitan, no good again. Reinstalled 10.9 Mavericks and upgraded to El Capitan, no good. Installed 10.10 Yosemite and upgraded to El Capitan, no good then finally got a 10.10.1 El Capitan usb, and upgraded to 10.10.6. Now its working. All Quicktime mov playing properly. Also during all the process, the quicktime works properly except installing straight to El Capitan from App Store. If I install Quicktime 7.6, movies also played well without errors except the Quicktime in El Capitan which consistently shows error (-101)
It does sound a bit strange. After reading your response, I decided to run a quick check of a drive on which I recently installed El Capitan. Last weekend I wanted to run some tests on my Mac Mini Server. It is still running under Lion and Server v1.5.0 app and I wanted to check out the latest Server v5.1.7 app. Unfortunately, this meant the tests had to be run under a more current OS, like El Capitan, but I wasn't willing to update the Mac Mini without preliminary testing. To get around this problem of circular logic, I popped a used 3TB drive into a docking station, erased it, initialized it with El Capitan, purchased/installed the newest Server app and ran my tests. However, it never dawned on me to test an app like the QT 7 Player app at the time.
In any case, I just logged in on that system/start-up drive and tested a number of MPEG-4 AVC files previously stored in the server's "Sites" folder. They all played without issue on the Mac Mini under last week's El Capitan install. Since your files now play fine, am wondering if Apple may have had a server download problem or if the ISP for your area has a significant "correctable error rate" problem in their equipment/lines. You may wish to keep an eye out for similar problems in the future just to be on the safe side. Seems like you had to go through a lot of work to get things up and running properly once again. Glad to hear all is well at this time...