I'd pull into the nearest port to fix them. Sometimes, either because of game coding or the amount of repair needed, you have to pull into a refit port or home port to affect proper repairs.
There are a number of issues with the stock game as well and many of those issues were resolved by upgrading to 1.5 and added some of the better mods such as TMO, RSRD, RFB and OM.
Mods also have certain orders in which they must be loaded so if you do use them make sure to read documentation very well as to mod orders and multiple mod compatibility.
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