Harvesters will only go to the town center that was built first. Even if manually ordered to go to a different one, they will not drop their resources there.
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Game currently stops when it finds the first town centre in the unit list. Need to compile a list of all available valid units for units to choose. Slated for version 0.1.5
Units will now go to the closest dropoff point. Fixed in SVN.
This is partially fixed in version 0.1.5; units will now drop off at the closest repository, not just the first anymore. But they still can't be forced to drop off at a specific site yet. Slated for version 0.1.6-ish.