If the update of the portable version is executed as indicated in the corresponding page, the previous version is included in the new one (can be verified via configuration > information). When executed under these conditions the executable belongs to the previous version and Slimjet is duplicated.
One way to solve this problem is to pre-copy the USER DATA folder before the upgrade, then completely delete Slimjet from the system or USB drive. Done this install the new version and on this copy in the same location USER DATA. This way Slimjet is not duplicated and the executable corresponds to the updated version.
Remember that USER DATA with all its contents hosts the configurations and extensions.