I really like Simple File Encryptor. I actually still use it for some quick file encryption. I'm happy to hear you are trying it out.
No, I don't plan on updating it. In fact, Ive ported a lot of the encryption functionality from Simple file Encryptor to Mini Mouse Macro. Have a look at the encrypt/decrypt function www.turnssoft.com/conditions.html#encryptdecrypt within Mini Mouse Macro.
I can't speak to the other tool your using to compare the encryption output. I'm not an expert in security but maybe they using different cypher's?
Im planning on releasing the source code for that too. When I do I'll post back and let you know. I haven't updating that app in over 7 years ... maybe i'll crack it open and check out the source code.
Sorry I don't have a solution for you and I don't plan on chasing this up in the short term.