Thank you all for you replies.
The dilution water is demineralized water that we've been using for a few years, so should be ok there.
We're actually using a combination of filters: 5um Pall nylon 30" depth cartridge style, followed by a 0.45um plate, with no charcoal at all. These filters are installed in series, in-line between the tank and bottling machine. They were pre-treated with peroxan and rinsed before passing the rum (first few liters of product are rejected).
The blackstrap does seem a likely culprit, which is unfortunate because it played three roles at once - color, sugar and flavor. The spice maceration was done in rum that had been diluted to the final 35% ABV.