Dynamic components are probably the problem.
This link is someone who was having a similar problem while patching (which is like a minor update)
Basically what is happening is that MSI has determined that the 'old' components have been removed (since they are dynamically generated, the GUIDs change every build). So in your upgrade it is removing the components you 'removed'. However it isn't laying down the new components, likely because it has determined there isn't a need for it to do so. You should examine your MSI file in Orca and look for the files/components that didn't get installed in your upgrade, and then search the install log for that GUID. That should give you a clue as to the next steps.
Also, here is the installshield best practice recommendations for Dynamic file linking.