I have noticed that there is a new preference in the RapidWeaver preferences labeled “Enable Smart Publishing” under the Publishing tab – it sounds like it’s for turning that exact feature.
As a developer I know there is a certain class of bug where a new control is added and connected to a new preference – when the preference doesn’t yet exist the button displays a default value and the app performs a default behavior – the bug happens when the default behavior and the default state of the button are not the same.
I do not know if that is the case here or not, but if I were the developer of RapidWeaver it would be the first place I looked. 
As a user, you can usually work around this bug by un-checking and then re-checking that checkbox. So, I’d give that a shot – if my guess is right it’ll fix the problem – if not you only wasted about 30 seconds trying. So, nothing (but 30s) to lose!
Isaiah