Thanks MC. I had a look at it but couldn't really figure it out. there was no negative body. We use a program called Viva to automatically assemble some models and it can be a real useless PITA some times. I ended up deleting the features I was pocketing and installing new ones and the problem just went away.Look in the tree at each part the pocket effects, and look closely at the icon for the PartBody where the pocket is.
If the green gear icon has a yellow '+' sign, than all the features behave as expected.
If the green gear icon has a yellow '-' sign, the PartBody is 'negative" and all features in it will behave with reverse polarity. As you said; pocket works as a pad.
To avoid this situation, don't have material removing feature (Pocket, Groove, Slot, Hole) as the first feature in the PartBody
If you have to have 'negative' PartBodies, then do a Boolean Assemble in order to have the pockets behave as pockets