I don't understand why this caused you problems - you had three things you could do:
1) Build/use your own freighters.
2) Build mass drivers.
3) Forego the minerals in favor of taking tax revenues.
John
Addressing this in reverse order so you can see where the lack of understanding arises.
3) Not a solution -- the minerals present on at least one of the bodies in question was very rare. Not a strategically sound option to let it go to waste. Nor is the alternative viable, buying the minerals, due to lack of income.
2) Had mass drivers, doesn't address the economics or strategic values in any way (in other words doesn't change the situation).
1) Building/using my own freighters to, presumably, carry infrastructure to the colonies so that the existing civilian line's ships would be useful and generate income, exacerbates the problem as it requires construction of additional infrastructure prior to shipping. Which costs money and, presumably, discourages or at least fails to encourage the shipping AI to build freighters. In other words, it encourages the shipping line to continue in unfavorable practices.
Now reading the context of my original quote, you can see that I tried alternatives such as placing shipping orders and providing subsidies to the original line. Even in the presence of the shipping orders, the line misspent the subsidies on building yet another colony ship it couldn't use instead of the freighter it could have used profitably.
Whether or not there is any connection whatsoever between shipping lines and civilian mines is beside the point. Somehow these civilian mines are being placed. I'm not providing the freighters for that operation. Should not the freighters be provided by the shipping lines for that purpose? Even if the actual shipping of the civilian mines continues to take place auto-magically, I suggest that a civilian shipping line owned and operated freighter be present for that purpose.