I've tested the scenario but cannot replicate the issue. Can you please send us to support at advancedinstaller dot com
the AIP (project file) and a verbose log
of such an installation so we can further test and investigate this?
Also, can you let us know if you sign the EXE setup package outside of Advanced Installer. This error may appear if you do sign the EXE setup package outside of the Advanced Installer. In this case the EXE will detect that the MSI embedded inside it doesn't have a signature, thus there will be a signature mismatch between EXE bootstrapper and its embedded MSI. In this case the installation will be aborted. If you want to digitally sign your setup package you should use only our "Digital Signature"
All the best,