Hi everyone, even if the thread is rather old, I'm posting here for the sake of completeness and in the hope this will help somebody.
I've experienced myself this problem in very similar conditions just a few days ago. It seems to be related to the "new" (by then!) .xlsx formats. Something has changed so that reading files in the "old" xls format works fine.
You should check if in those apparently empty rows there is some kind of formatting that avoids excel consider them really empty (borders, fonts, etc). Sometimes an user might select the entire sheet and apply Calibra or Arial font family.
In my case, I noticed that the job was loading more 11.500 while in fact the file contained less than 300 rows of data.
I decided to make an attempt by deleting some blank rows and saw that the number of total processed rows decreased. So I went on by deleting 11000 rows that looked empty but in fact were somehow different, and everything worked fine.
Another way to solve this could be re-save the file in the previous .xls format, as this issue seems to refer to newer formats only. Ah, you should delete entire rows, not cells.