UPDATE: After testing the suggested options in the firmware with no noticeable results, I changed my stepper motor to a higher torque Nema23 motor (425oz-in / 2.8N.m). Well that had no noticeable effect either. I was still losing steps on the Z axis at a very slow rate. Note that this is only noticeable on larger 3D carves.
I read an article on the Community Form where @chrismakesstuff mentioned that with the launch of the SLB they moved from 8 micro steps to 32 micro steps and that there should be no effect on performance. In a last ditch effort I changed my micro stepping back to 8 and tested the same 3D carve as before. Guess what? No more lost steps. The carve remained level to the end (well i stopped at 65% - it was getting late for this old man 
).
I went back to higher noise like I had on the original Longboard but I can live with that. The accuracy seems to be the same as before, although this was a simple carve so will have to eventually try a more intricate model.
For now I am leaving as is. I may eventually try micro stepping at 16 but that will be a future experiment.
Hope this helps others in the future.