Ok, you are correct, the "Nov" version does not allow "CNTRL+Key" for scene hotkeys at all - however, the "Feb" version does, and this is where the problem exists. When we created our scenes with the "CNTRL+Key" combinations, we did it in the "Feb" version and that is when we noticed the issue. When the file wouldn't load, we moved to the "Nov" version and had hoped it would load with that version, however it would not load.
Now, in our scene files that we created with the "Feb" version, we also had "SHIFT+Key" combinations, but the "Nov" version doesn't recognize (WILL NOT TRIGGER WITH SHIFT) those combinations. The November version will allow you to bind, for instance, "R" as a hot key and also "r" - however, it will not trigger the "R" with the "SHIFT+r" key combination, you have to hit "CAPS-LOCK-ON" then "r" to trigger "R", it will not trigger with "SHIFT-r". This is the reason why we have to go back to the "Feb" version as the "Feb" version works fine with "SHIFT+Key" combinations.
With that said, it now appears that maybe this "CNTRL+Key" issue came up sometime long ago in the past and as a quick fix the developers completely removed all "KET+" combinations which broke the "SHIFT+Key" combo in the November version.
Attached (link) is a scene file with 2 blank scenes, but with the "CNTRL+Key" combos active so you can see what it is doing when loading the file.
http://csmansys.com/F.zip