Ok, I think I fixed it [well, the save file at least].
I changed:
<accumulatedPlayerTradeValueForPositive>4409450.5</accumulatedPlayerTradeValueForPositive>
<accumulatedPlayerTradeValueForNegative>4419115.0</accumulatedPlayerTradeValueForNegative>
<totalPlayerTradeValue>4419115.0</totalPlayerTradeValue>
to:
<accumulatedPlayerTradeValueForPositive>0</accumulatedPlayerTradeValueForPositive>
<accumulatedPlayerTradeValueForNegative>0</accumulatedPlayerTradeValueForNegative>
<totalPlayerTradeValue>0</totalPlayerTradeValue>
and deleted the 2 transactions relating to the purchases from Qaras' black market:
<TransactionLineItem id="112947">
<id>food</id>
<itemType>BOUGHT</itemType>
<cargoType>RESOURCES</cargoType>
<submarket class="Submarket" ref="32938"></submarket>
<quantity>436.0</quantity>
<price>4349.0</price>
<tariff>0.0</tariff>
<demandPrice>0.0</demandPrice>
<demandTariff>0.0</demandTariff>
<timestamp>-55048845053000</timestamp>
</TransactionLineItem>
and
<TransactionLineItem id="113022">
<id>heavy_machinery</id>
<itemType>BOUGHT</itemType>
<cargoType>RESOURCES</cargoType>
<submarket class="Submarket" ref="32938"></submarket>
<quantity>10.0</quantity>
<price>1686.0</price>
<tariff>0.0</tariff>
<demandPrice>0.0</demandPrice>
<demandTariff>0.0</demandTariff>
<timestamp>-55048845053000</timestamp>
</TransactionLineItem>
Kind of amazed that I managed to find the pertinent data in a 16MB file! and that changing it had the desired effect.... on my 1st attempt too!
So yeah, it was definitely the blackmarket purchases that caused the problem.
Hopefully that info will help in reproducing it, and locking down what's causing the rep loss of these particular trades to be processed ad infinitum.
It'd be interesting to see if the problem recurs in my save the next time I buy from Qaras' black market.