Ah, is the 2da file that's in your override readable in notepad? If so, these are called v2.0 2da files and KSE only knows how to read v2.b 2da files. You can convert between the two by opening the v2.0 2da file in Excel (space delimited) and then "Write 2DA" using the Excel 2DA Add-in available from http://www.starwarsknights.com/tools.php
Did you try creating a kse.log file for KSE to write into? In windows explorer just right click and choose New->New Text Document and then rename the file to kse.log and say yes when it asks you if you want to change the extension. Then try opening KSE again (with spells.2da in the override). After KSE crashes, look at the contents of the kse.log in notepad.