Can you post the model itself? If not, can you post some screen shots of the area where you feel that bonded contact isn't being enforced?
are you saying global bonded doesn't work but bonded contact sets does work?
are you sure that all the faces are touching?
my suggestion is to turn global back on and start suppressing your contact sets to find which ones aren't staying connected.
i did run into some cases where the sheetmetal bonding wasn't happening everytime and those were bugs that i reported to solidworks. (for you, through your reseller)