In ElecKey Integrator/Protection Options dialog box, there is the option "Enable Self Checksum to Protect Against Code Modification". It enables the system to perform integrity check of the executable to protect against tampering, modification, and virus infection. The code signing causes the checksum to return invalid in this case. You can disable this option if you want to code sign your exe.

You must use ElecKey Integrator to protect your app before code signing. In addition, when using the Integrator to protect your app, you must also disable the option "Enable Self Checksum to Protect Against Code Modification" under the code protection settings.