When I enter the optional Signature/User Code in the programming options when creating the JEDEC file (i.e., running Hprep6), it is not entered into the JEDEC file.
This is a known issue that only affects the automotive 9500XL devices (XA9500XL). The non-automotive devices (XC9500XL) are not affected.
To work around this issue, the required Signature/User Code should be entered as follows into the "Other Programming Command Line Options" of the programming properties box: -n followed by the signature (restricted to 4 characters; i.e., -n rev2).
This issue is to be fixed in a later version of ISE.