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In an hourly EPW file, the first entry is for hour 01:00, because it assigns weather data for the first HOUR of the simulation (STARTING at 00:00 and ENDING at 01:00). For your case of using minute intervals, the first entry assigns weather data for the first MINUTE of the simulation (STARTS at 00:00 and ENDS at 00:01) instead. To follow the same convention as the hourly EPW files, your first minute-interval entry should have a time stamp of 00:01, not 01:01.
Really, EnergyPlus is reading the data at the correct intervals (shown in the simulation results). My hunch is that it's offset by one hour too late in your minute-interval EPW file.