Data not acquired during conditioning phase

we usually run a conditioning method before starting the analysis. lately we have encountered a problem regarding the acquisition data during this method: the method stops acquiring any data (i.e. pressure, current, PDA) 1 min after the injection phase starts. In fact the system switches to "Pause" mode and remains that way for all 40 mins (the overall duration of the method), so practically there is no conditioning at all, as the capillary stays in Buffer position A1 for all the duration of the method (so for 40 mins). Data acquisition is fine when we then run samples. Why is this happening? thanks in advance