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theres octalink for road and octalink for mtb, dont know if that could be your problem....!
http://sheldonbrown.com/images/bbsx4-labeled.jpg
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theres octalink for road and octalink for mtb
The difference between road and MTB is just axle length. The Sheldon Brown picture shows early & later Octalink, and applies to both road & MTB. The early version has short splines which proved too weak, so Shimano issued a second version with much longer splines and kept very quiet about the appalling balls up they had made of the first version.
Fitting a 6500 crankset to a 5500 octalink bottom bracket, should be compatible, but can't get the splines to slot in so the cranks are aligned. Can't see any damage on either - am I missing something? Would rather not have to shell out for a brand new bb