The discrepancy is due to daylight savings time. (And there are differences for many hours during the summer, not just near midnight.) Delete this object and the values will align perfectly:

RunPeriodControl:DaylightSavingTime,
April 7,                 !- Start Date
October 26;              !- End Date

If this is measured data, then you want DST to be off, because it's likely in synch with the sun using standard time. If this is calculated data, then you might want the values to be shifted for DST, but that can get confusing.

I applied all your comments on the file, and still have the same issue in the schedules. I uploaded the files that I used earlier based on your comment and also the output.csv file. I am observing one - hour forward shift in the output schedule that I am exporting. Also, if I realign the data manually, still there are intervals that those input and output schedules are not the same.

https://drive.google.com/drive/folder...

In the 1minSchedule file which I am trying to reach that. From beginning the 0.0001 values that I have in that file are only because not to use zero value there. The only data that I have is from Jun-Aug.

(It would have been helpful to see a graph showing the discrepancy).

Anyways, from a cursory look I'd say your Output:Variable is wrong. Here's what you have:

Output:Variable,
    *,                       !- Key Value
    Schedule Value,          !- Variable Name
    Timestep,                !- Reporting Frequency
    MiscElecLoad_1;          !- Schedule Name

I suspect you don't understand what Schedule Name actually does. See the I/O Reference Guide, but in short:

The output variable will be active during any hour in which the schedule value is >0

If you want to report only one schedule named MiscElecLoad_1 you should do it like so:

Output:Variable,
    MiscElecLoad_1,          !- Key Value
    Schedule Value,          !- Variable Name
    Timestep;                !- Reporting Frequency

Edit:

I loaded your 1minSchedule.csv file using Python (with pandas), and I filtered it to find the timestamps where you have a 0 value, meaning the Output:Variable doesn't report. It happens for only 6 values, all of which are around 23:30:

2005-06-12 23:32:00    0.0
2005-06-12 23:33:00    0.0
2005-06-12 23:34:00    0.0
2005-06-12 23:35:00    0.0
2005-06-12 23:36:00    0.0
2005-06-12 23:37:00    0.0

So that explains your problem between 23 and 24.

Edit 2:

In the output you show, you never include the timestamp, but your SimulationControl has Run Simulation for Sizing Periods:

  SimulationControl,
    Yes,                     !- Do Zone Sizing Calculation
    No,                      !- Do System Sizing Calculation
    Yes,                     !- Do Plant Sizing Calculation
    No,                      !- Run Simulation for Sizing Periods
    Yes;                     !- Run Simulation for Weather File Run Periods

This means that your eplusout.csv will include, at the top, data for your sizing periods. This could cause an offset when you are comparing stuff.

I did test do dummy example hourly schedule that I added to the example file 1ZoneUncontrolled.idf and I got this misalignment schedule initially (actually I found it because the output length was not 8760 but 8808 since I had two design days in my file (8670 + 2*24hrs = 8808).

After realigning the data (or just not run it for Sizing Periods), the input matches the output perfectly.