Hi Altherr,
This sounds like a Directory Table issue. Can you post a few things so we can see what's going on? Namely:
1. The Custom Action details--what property is it setting, and what property is it getting the value from?
2. What is the Directory Parent in the Directory table of the property you're setting? If you don't know, open the MSI in Direct Edit mode, and go to the Direct Editor's Directory table.
Let me know if you aren't sure what I'm talking about, and I can PM some more detailed instructions. Or, you an post the uncompressed MSI file that results from running: msiexec.exe /a "c:\package.msi"