Missing Join Tables after Upgrade from CE 6.2.2 to 6.2.3

[ldebaets]

I did an upgrade from version 6.2.2 to 6.2.3 CE and there were two missing missing tables for modules in a custom package. It happens for the case of two modules having a one-to-many relationship with another common module. I have two such cases. The relationship table shows the problem and a picture is attached.

I checked the metadata files that were generated by the modulebuilder and they are correct. I believe the moduleinstaller could be making an error and using the previous join table that was created for the right-hand-side module instead of using the name of the join table for the new relationship table. This join table existed correctly in the 6.2.2 application database.

Please help! There is a requirement to be able to do upgrades of existing applications and installs of the custom package for new applications to be deployed.

I'm running on a LAMP stack with Ubuntu: PHP Version 5.3.2-1ubuntu4.9, Apache version 2.2.14, MySQL API version 5.1.41.

The problem appears consistently and even for installs on the latest 6.3.0RC3 load.
There is no sign of a problem in the Apache or sugar logs (which are on in Debug mode).