Software Deployment

I have a problem with repairing a package, the package is RasterCAD. I'll try to explain the process that we follow here first as it's always worked perfectly until today!

• Deployment is done via sms 2003
  
• We obviously create transforms for vendor apps. When we create a transform we have an internal company version for this (no change to ProductVersion property). For our first deployment this is version 1 then if we need to make changes to the same package without deploying a new version of the vendor app it becomes version 2. e.g
  RasterCAD_11.0.0_BE_v1.msi - initial version
  RasterCAD_11.0.0_BE_v2.msi - Updates required to user files and permissions
  
• When we deploy these types of updates we tend to have a pre-requisute vbscript that sms runs to determine if Version 1 is installed or advertised and if it is uninstalls it. Then sms continues and installs version 2

For RasterCAD the vendor package has an internal cab file. I have added files to the package which I have done in an external cab file (again no issues with this).
RasterCAD contains files in the users profile and HKCU keys so on first run it repairs. as I say never been a problem before but the install fails because it cannot locate the external cab file. But it is looking at the distribution point for RasterCAD_11.0.0_BE_v1 rather than RasterCAD_11.0.0_BE_v2.

I've looked in the registry HKLM\SOFTWARE\Classes\Installer\Products\GUID\Sourcelist\Net
and see 2 entries
1 - value \\Server\share\Folder1 - this is the distribution point for BE_v1
2 - value \\Server\share\Folder2 - this is the distribution point for BE_v2

My understanding of this is that the package would check both areas and find the CAB file in \\Server\share\Folder2

If I check the reg settings for other packages we've done there are loads entries under the Net key and there are no issues.

Sorry for the long explaination but does anyone have any ideas on why this may be happening?

Cheers
Rich