Extra rows in worksheet

Hi there, I'm using Excel for holding lots of numerical data. Another software program pulls the information from Excel and is used to evaluate the data. The problem I am having is that some of the worksheets in my workbook have extra rows, and by "extra" I mean over 1,000 extra, blank, empty, rows. This means that in the other software program, it pulls over thousands of blank cells that have to be deleted every time it is opened. I've cleared the formatting for the extra rows, and still haven't found a solution.

Hightlight sheet, sort by A-Z. It should push all the empty rows to the bottom.

The range is defined by column header in Excel...the number of rows it pulls over is based on the number of "active" (for lack of a better word) cells/rows in Excel...For example, if I have data entered in Columns 1-3, rows 1-10, the other software will pull the information from the exact same range. However, in my problem worksheets, I have data entered as mentioned before, but the other software is pulling data from columns 1-3, rows 1-1456. In my problem worksheet, the vertical scroll bar in Excel automatically shows rows 1-1456, rather than just one full page or what I have data entered through. When coupled with the knowledge I have of how the other links and worksheets work fine, I really believe this has something to do with Excel rather than the other software. It is as if Excel thinks there is something in those cells, but there isn't, at least not that I can find.

The empty rows appear below the last of my data.