My guess is you are a victim of the compartment efficiency associated with the long repair times mod. The values for the TypeII bow torpedo room which coincidently overlaps with the TypeVII and IX damage control were very carefully selected to get the desired torpedo loading times (with the torpedo loading times adjusted as necessary).
I can't tell you exactly what the problem is if the long repair times are the culprit, but I can suggest looking at the Interval1 value in the basic.cfg.
We're wrestling this the balance issues associated with this particular mod now. Unfortunately we haven't yet come to a decent solution that gives extended repair times without breaking some other part of damage control or crew management. This is going to be a very tough one to balance, and the compartment overlaps are a big culprit.
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