I think my answer was essentially sitting in another thread (http://vpuniverse.com/forums/topic/1339-dmd-issues-with-potc/?hl=setup.exe#entry11977) where arngrim stated "you would need to check this cabinet mode option from the f1 options when you play, for the tables that you already launched before you had the default settings with cabinet mode checked"
It seems that I will need to edit all previously loaded tables on my cabinet that use the DMD display.
I'll add some steps below in case this might be able to help someone else in the future:
To fix the DMD positions and have them remember their positioning, when using VPinmame.dll for SAM tables, I need to;
1) Open the table and reposition the DMD by 'click and drag' to the desired position/screen. (TIP: If doing this in Hyperpin, press 't' to be able to view your cursor)
2a) Press F1 when the table is in focus, to bring up Game Settings
2b) Right click on the DMD, and select Game Settings
3) Select 'Cabinet Mode' and click 'OK'.
Changes are not immediate. To see the saved settings, you'll need to exit VP and/or Hyperpin and reopen the table via VPinball and/or Hyperpin. Settings should have saved and DMD should be in the correct position.
You'll need to perform the steps for every table that has it's DMD in the wrong location. I do not believe you'll need to exit VP or Hyperpin to see the saved settings between each table, but you might want to check to be safe.