Mmm, strange. What happens when you make the Part Body the in work object and then hit the update button - does the model fully re-build?
Try this, create another body and put a pad in it that represents the hole. Then do a Boolean operation to remove this body from the original thick surface and see if this leaves you with a part with a hole in it. Bit difficult to tell what it might be without seeing the part or the spec tree - could be worth cleaning the part (File - Desk - Right click on the parts and then select CAT5DUA. Select Clean and then hit Run. Once the utility has run, refile the part in the usual way).
Also, make sure all of your surface are in No Show, if the parent element of the thick surface is visible you won't see the hole.