Following on from many questions on the Moodle forums and many days\hours testing. I am finally able to post back in here my experience so that if others have this then they can save themselves time.
New Spinups I have been doing on the Moodle 3.3.2 base
Bootstrap 2.3.2 coding and simple HTML coding
that should be working was not.
This then would lead to major redevelopment of courses that carried this code and that was something that was not acceptable due to the time and costs involved.
After hours of testing on existing systems, 3.1.1- 3.2.2 and various 3.2.2 systems that were run both on VM and local in-house servers. Finally have a 3.2.2 base working as it should.
My suggestion is to use some base Bootstrap 2.3.2 code on a new VM startup to see if there is any corruption with in the base codes before you load in any plugins and or courses you may have developed.
Any of these codes will give you an indication.
Bootstrap 2.3.2 codes
thanks to the Adaptable theme crew for providing some quick codes that can be used in Marking block setting to test this too..
Basic styles for marketing blocks
Advanced styles for marketing blocks (Tabs)
If all of these work then you have a clean Moodle 3.3.2 base to start working off.
If they dont..
I suggest you don't waste hours trying to debug the problem as its way deeper then the time it would take to find.
Personally I have spent countless hours trying out fix's that only lead to more problems and crashes.
Just shut down the server and start another one.. Test all of above again.
For the Bitnami team.
I have kept a server with 3.3.2 going that seems corrupted, if you want to take a look.
I can give you access to it so you can maybe see why this would be happening.
I haven't changed any back-end code apart from increasing file uploads and forum post sizes.
As with any upgrades this has been a frustrating experience but finally got to where we need to be and can get back to enjoying actually course creation verses the horrible back-end server problems..
That why we LOVE Bitnami\AWS so much!!!!!