This is not at all unusual because Excel will only store a record in the file for a cell if that cell actually contains something (crudely, it is a little more complex than this of course!). If the cell is indeed blank, then it is highly likely that there will be no cell record for it in the file and that POI is correct in returning blank.
There are a couple of ways to check whether this is truly the case, which one you use depends upon the file type.
If you are working with an OOXML format file (.xlsx) then this is simply zipped xml and you can use a simple tool such as PKUnxip or WinRAR to unzip the archive. Next, you can navigate through the folders until you find the xml markup for the sheets - likely to be in a file with a name like sheetn.xml where n is the number of the sheet, so 1, 2, 3, etc. Open the xml with an editor and look for the cll record that corresponds to the cell you think is POI is miss-reporting.
Option 2 relates to the older binary format (.xls) files and does rely on another POI tool called BiffViewer -
http://poi.apache.org/apidocs/org/apache/poi/hssf/dev/BiffViewer.html - which can be used to view the contents of the file. Again,
you should be able to check to ensure that the cell records are indeed there.