This article applies to all supported versions of API Gateway and OAuth Toolkit.
As upgrades are done to the individual components within the Solution Kit, the version on each component will reflect it's own version. Since the Solution Kit itself (the parent level) is not upgraded specifically, the version it displays is just the original version that Solution Kit started at / was installed at. This suggests that the OTK was installed at version 4.0 but the components have such been upgraded to 4.1.
This discrepancy in version display not cause any issues, but a support case can be filed if there are further concerns about this.