A fix for this was included in 2013 Update1.
I have just started getting the same problem on Inventor Professional 2012, SP2 (Autodesk Product Design Suite Ultimate 2012). Create is enabled but does not add any new holes to the table. Any help is appreciated.
I'm pretty sure I installed all relevant hot-fixes before and after SP2. I observed the following:
All holes are picked up if creating a new hole table (View). If one hole reference is deleted it cannot be added back, the only way to list it in the table is to create a new table for that view. I don't use this dimensioning method very often therefore cannot say when this problem occurred.