I tend to drive the Blue Marlin on as well (in a marina - no rips or anything), although by the time the graunching noise started on saturday, it was too late.
I'm beginning to think that maybe the rollers are too loose and can flip over - and I should do them up tight in position while I've got the RIB on the trailer. Also, I don't think it's practical to get almost 2 tonnes of RIB out of the water without getting the bearings wet - I'll just make sure that I pack them with grease and service it regularly. When completely out of the water, on the flat, she's heavy enough that I can't move her backwards or forwards on the rollers. I have to winch her along and back again.
My biggest fear isn't scraping the transom as she comes off - but the outdrive leg. It hangs well below the transom bottom even when cranked up to the trailer position.
In future, I think I'm going to go for the innundation approach, and submerge the trailer and allow the water to take some of the weight of the boat as she comes up on to the rollers. At least that way the chines should ride up on the rollers rather than digging in and damaging the hull.
The trailer is the standard trailer supplied with the boat, so I suspect think it's mostly down to operator error and lack of experience.