I was diff'ing a 2000 line, 25 column spreadsheet and and got:
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
I fixed it by altering the excel_cmp.bat file to give the java virtual machine more memory by adding -Xmx1024m to the options passed to the java command:
java -ea -Xmx1024m -cp "%dirname%\dist\*;" com.ka.spreadsheet.diff.SpreadSheetDiffer %*
Can I suggest this is rolled into your next update to cover this problem for others?