Repairs on multiple buildings happen in the same turn, constructing buildings follows the queue, one won't start till the one before it is finished. Same with retraining vs training. If you give the command to build/train, and then repair/retrain, the repair/retrain will happen that turn regardless of the queue, even if the repair/retrain involves multiple buildings/units. Building/training will wait till each preceding one is done, but repairs/retrains are done immediately. Sometimes a damaged building will allow retraining that a less-damaged one at another time will not. At least, that is what seems to happen, I may be wrong.
You don't have automanage turned on, do you? If so, turn it off and see if that solves the problem.
You are playing just the standard Rome Total War, right?
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