It could be an issue with the source excel file. I had the same issue recently when trying to upload the data. After trial and error I managed to tally the records between the excel file and the table.
Open your excel file, go to the last record in the sheet, select all the rows below the last record (technically all empty rows) and delete it. Re-run the script and see if the count matches.
This worked for me but honestly I am not sure why it causes such a problem in the first place.
Hope this helps.
Below are the possible cases:
1. If you using Cross function for loading, please check is there any null values exist on the Data field values. Cross table wont load the Null values. Use Isnull condition to convert null value in the zero.
2. In Table Boxes, QLikview will show unique values only. Use Row No or Rec No function to create the unique key on the the each row.