My idea: Does the .xls have VBA code in it? I've occasionally written code that filled up an entire worksheet with data—some of it blank data, but data nonetheless—when I meant to do it only to the first thousand rows. Maybe you copied a bunch of blanks all the way down to the end of the worksheet and thought it didn't matter because they were blanks. Just an hypothesis.

My son's idea: Check your "page file". I'm a Excel geek, not an OS geek, so I'm pretty sure page file has to do with handling RAM swapping (ie for virtual memory) but can't add much to that. If you want to pursue this, let me know and I'll ask him for more detail.