What is the "printable area" of the documents?
A spreadsheet in excel will always show all these extra cells, but generally, only those cells with formatting or data will be saved or printed.
Selecting the cells and deleting them will still leave all those extra cells visible, but they should only be printed if they actually contain data.
After deleting the extra cells to clear the data, does what shows up in Print Preview change any?
UPDATE response to comment:
Does the Print Preview show all the extra, unneeded pages that the batch process will end up printing?
Print Area is not the same as page setup. Print Area is the section of the document that can be specifically defined as should be printed when you issue a print command on that file.
In Excel 2003, setting the print area is in the File menu, Print Area, Set Print Area. Select "Clear Print Area" to remove any hard-set print area commands.
In 2010, Print Area is in the Page Layout ribbon, Page Setup section. You can clear the print area here too.
Once you've cleared the print area, Excel is free to determine what ought or ought not be printed by itself. So long as the cells have been cleared of data or formatting, the default print area should shrink to the area actually inhabitted by data.
UPDATE more comments:
At this point I would assume the documents themselves have some sort of corruption going on.
After making the above changes, you may try the "Open and repair" option to try and repair the files. If that fails, copy the data to a new spreadsheet.
I would be interested to know what happens when the batch process prints a "normal" spreadsheet that has not had this issue.