Put the files from the engine demo back, and determined root cause of the issue, and corrected a few minor issues with the CountedPtr and verified the previous results were still valid and they are.
I found one last outstanding issue with the CountedPtr test and fixed here. CountPtr is still the same speed or slower than a raw pointer (depending on the location of the reference counter) and std::shared_ptr is still 2x to 4x slower. I also re-ordered the tests in order of theorhetical speed, fastest first.

In release:
The objects being created all chenage a variable on destruction and have initializing, but otherwise trivial constructors. This is useful only for comparing the speeds of the point constructs on this platform, not for providing objective pointer dereferencing costs.
1 - Creating and Dereferencing a raw pointer 1000000 times with external counting took: 32801 Microseconds
2 - Creating and Dereferencing a CountPtr 1000000 times with internal counting took: 32736 Microseconds
3 - Creating and Dereferencing a CountPtr 1000000 times with external counting took: 65183 Microseconds
4 - Creating and Dereferencing a shared_ptr 1000000 times with external counting took: 83694 Microseconds
5 - Creating, Dereferencing and Copying a raw pointer 1000000 times with external counting took: 32286 Microseconds
6 - Creating, Dereferencing and Copying a CountPtr 1000000 times with internal counting took: 32506 Microseconds
7 - Creating, Dereferencing and Copying a CountPtr 1000000 times with external counting took: 64409 Microseconds
8 - Creating, Dereferencing and Copying a shared_ptr 1000000 times with internal counting took: 103198 Microseconds

In Debug:
The objects being created all chenage a variable on destruction and have initializing, but otherwise trivial constructors. This is useful only for comparing the speeds of the point constructs on this platform, not for providing objective pointer dereferencing costs.
1 - Creating and Dereferencing a raw pointer 1000000 times with external counting took: 36013 Microseconds
2 - Creating and Dereferencing a CountPtr 1000000 times with internal counting took: 56645 Microseconds
3 - Creating and Dereferencing a CountPtr 1000000 times with external counting took: 91505 Microseconds
4 - Creating and Dereferencing a shared_ptr 1000000 times with external counting took: 123324 Microseconds
5 - Creating, Dereferencing and Copying a raw pointer 1000000 times with external counting took: 37030 Microseconds
6 - Creating, Dereferencing and Copying a CountPtr 1000000 times with internal counting took: 71103 Microseconds
7 - Creating, Dereferencing and Copying a CountPtr 1000000 times with external counting took: 109021 Microseconds
8 - Creating, Dereferencing and Copying a shared_ptr 1000000 times with internal counting took: 159026 Microseconds
Replaced all the auto_ptr with CountPtr, and added shared_ptr via make_shared and it does much better. Still slower than intrusive reference counting though. I also touched up the binary buffer and I am preparing some tests for it.
Debug:
The objects being created all chenage a variable on destruction and have initializing, but otherwise trivial constructors. This is useful only for comparing the speeds of the point constructs on this platform, not for providing objective pointer dereferencing costs.
1 - Creating and Dereferencing a raw pointer 1000000 times with external counting took: 36579 Microseconds
2 - Creating and Dereferencing a CountPtr 1000000 times with internal counting took: 55174 Microseconds
3 - Creating and Dereferencing a CountPtr 1000000 times with external counting took: 95658 Microseconds
4 - Creating and Dereferencing a shared_ptr 1000000 times with external counting took: 123791 Microseconds
5 - Creating and Dereferencing a shared_ptr from make_shared1000000 times with external counting took: 235269 Microseconds
6 - Creating, Dereferencing and Copying a raw pointer 1000000 times with external counting took: 36710 Microseconds
7 - Creating, Dereferencing and Copying a CountPtr 1000000 times with internal counting took: 72871 Microseconds
8 - Creating, Dereferencing and Copying a CountPtr 1000000 times with external counting took: 105936 Microseconds
9 - Creating, Dereferencing and Copying a shared_ptr 1000000 times with internal counting took: 156729 Microseconds
10 - Creating, Dereferencing and Copying a shared_ptr from make_shared1000000 times with external counting took: 273992 Microseconds

Release
The objects being created all chenage a variable on destruction and have initializing, but otherwise trivial constructors. This is useful only for comparing the speeds of the point constructs on this platform, not for providing objective pointer dereferencing costs.
1 - Creating and Dereferencing a raw pointer 1000000 times with external counting took: 32182 Microseconds
2 - Creating and Dereferencing a CountPtr 1000000 times with internal counting took: 32760 Microseconds
3 - Creating and Dereferencing a CountPtr 1000000 times with external counting took: 65457 Microseconds
4 - Creating and Dereferencing a shared_ptr 1000000 times with external counting took: 83875 Microseconds
5 - Creating and Dereferencing a shared_ptr from make_shared1000000 times with external counting took: 54373 Microseconds
6 - Creating, Dereferencing and Copying a raw pointer 1000000 times with external counting took: 32293 Microseconds
7 - Creating, Dereferencing and Copying a CountPtr 1000000 times with internal counting took: 40137 Microseconds
8 - Creating, Dereferencing and Copying a CountPtr 1000000 times with external counting took: 65237 Microseconds
9 - Creating, Dereferencing and Copying a shared_ptr 1000000 times with internal counting took: 102422 Microseconds
10 - Creating, Dereferencing and Copying a shared_ptr from make_shared 1000000 times with external counting took: 71023 Microseconds