Oh, you must be on 2.0, since the 2.1 branch doesn't have a data-updates script. I suppose I could backport some of the new code from 2.1 to 2.0, see if it works with the old Pipebelts API...
EDIT: Oh, the issue might be with the Pipebelts API mod itself, either not copying some transport belt because of load order, or some other unknown issue. I don't really want to spend any more time debugging this, since the old code isn't 1:1 compatible with the new code. I suppose it would help to know what other mods you have that add transport belts, could maybe fix it by forcing a load order, but no guarantees.