Carnet problems
I believe that taking one of the popular entry ports into Indonesia with a motorcycle, you probably won't have problems. People are doing that all the time, e.g. Peninsular Malaysia to Sumatra, most likely West Timor to East Timor.
Leaving Indonesia appears to be a lot easier than getting in (not surprising).
Based on my experience, also Sheen Kua last year ( By Bike to Malaysia) there's a good chance you will have trouble in Borneo. If you assert that the carnet system has in fact been ratified by Indonesia, I highly recommend taking official documentation stating same. Otherwise it comes down to your word against the custom official, in his office. A letter to that effect from the consulate would probably help a lot.
As per previous advice, a letter of invitation from an Indonesian bike club will also grease the wheels.
My agent paid RP1M in "fees", although officially there are no fees at all. I would try to avoid agent next time - it pretty much a guarantees that you will pay fees, whereas you may well get through cleanly by yourself. Trouble is, going by cargo boat makes it difficult/impossible to enter without an agent. Much cheaper to skip Borneo altogether.
None of this is an issue if you are entering by ferry, which means that Borneo cannot be your "port of entry" into Indonesia. Have heard from a regular rider (local) that road crossing from Sarawak to Kalimantan is even more "expensive" than my experience, but I'm almost certain he was not travelling under a carnet, so that option remains to be documented.
cheers
Colin
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