@xbastek To us it seems like the most likely explanation is that the timezone settings in IDE have been changed to users local time. The crystal used within the RTC is of quite high precision, and the time drift we have observed in testing has been on the order of one second in several months. In addition, the particular nature of the time drift (that is, in hours) would point this way as well.
The Mervis IDE as well as Neuron itself runs on UTC, but this is possible to change in the PLC setup, which will naturally skew the clock. Would it be possible to check that the customer's PLC time corresponds to UTC? If not we would recommend to set it back to UTC and see if the issues persist.