I've been gradually increasing my independent rep (from -100), and finally got it up to suspicious so I could take missions from all independent characters.
- I took a couple of independent missions to Killa (from Chicomoztoc; 3000 Domestic Goods, 300+30 Heavy Machinery)
- I then took a single independent(covert) mission to Qaras. (500 organs)
- Then from Qaras I took 2 more missions for the independents back to Killa. (I bought the needed supplies from Qaras' blackmarket; 500 Food & 10 Heavy Machinery)
- Completed the missions to Killa.
I then began getting repeated reputation hits from both the Pirates (due to smuggling), and Independents (due to trade with Qaras).
These reputation hits have occurred 5 times so far; the exact reputation cost seems to be variable.
Save here (made after I'd experienced 2 rep hits, hopefully whatever state is causing them has been saved too)
https://dl.dropboxusercontent.com/u/54785909/starfarer/0.7.2a%20RC3/save_TJJ_1837487541392700808.zipI suspect the cause might be delivering an independent(covert) mission to a pirate base (to whom I had a positive relationship with)?
:edit:
Just to confirm, I've continued playing after the point that save was made, and the rep hits have continued for months.
The Pirate rep eventually bottomed out at -50 (presumably the lowest you can go with the Pirates 'due to smuggling').
The Independent rep has continued to fall, further into Hostile, eventually bottoming out at -75.
Once bottomed out, the reputation messages stop.
However if my reputation ever increases above these minimums, the rep hit events will begin again.