Normally, the Modified By and the Signed By should always be the same. Unfortunately, due to the way the Lotus Notes API works, this is not the case for local databases when the design is signed with an ID different from the user's actual ID.
For example, in this screenshot we see that two images have been signed by Alfred Test1 yet the last modification was performed by Alain Test5. In this case, signEZ was first launched with the ID 'Alain Test5' and we chose to sign with Alfred's ID. This kind of situation only happens with local databases.
In short, if you do a switch ID to process on a local database, it will sign correctly, however, for reasons that remain unclear, the Notes API will set the Modifed By value to the user's actual ID.