As stated above, mention it to them and worth a quick fault check but if the battery has been flat the gearbox (and any other) ECU can lose it's basic settings. This means it has to "learn" all travel stops of actuators and sensors before it can perform properly again. It is not uncommon to need to carry out basic settings on the diagnostic computer after a flat batt. The car can usually get around this itself but can take 30-70miles which may explain why it drove ok first off.
A quick note. If ever jump starting ALWAYS turn on all heavy consumers AFTER the flat car has been started but before disconnecting the cables. This is due to the fact that when the cables are disconnected and the system's charging there is always a small spark from the clamps. This spark can cause a voltage spike around the car's electronic systems and seriously damage ECU's!!! Any of them!
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