Just to update I have found that the problem seems to stem from the torch call 
and if I use the wixmst file generated by 3.5 it creates the patch fine.

Here is my torch call:

"%WIXDIR%\torch.exe" -p -xi "%PatchSourse%PROGRAMx32.wixpdb" 
%NewInstall%x86\PROGRAMx32.wixpdb -out %OutputFolder%\PROGRAMpatch32.wixmst

Not sure if this helps at all

-----Original Message-----
From: ChipSlog [mailto:steven.par...@nikonmetrology.com]
Sent: 25 September 2012 14:34
To: wix-users@lists.sourceforge.net
Subject: Re: [WiX-users] [WIX-users] Patch in Wix 3.6 is empty. warning 
PYRO1079: The cabinet '***.cab' does not contain any files

Did you have any more luck with this issue Leo?

I have the same problem after upgrading to Wix 3.6, nothing has changed, I 
still have the same patch family. In 3.5 it picks up the fact that the versions 
have changed on multiple files and adds them to the patch however in 3.6 it 
comes up with the empty cab file warning.

<?include X:\Utils\UtilsInstall\VersionInformation.wxi ?>
  <Patch
      AllowRemoval="no"
      Manufacturer="*****"
      MoreInfoURL="*****"
      DisplayName="*****"
      Description="Update Patch for $(var.ApplicationVersion)"
      Classification="Update"
        >
    <Media Id="5000" Cabinet="Patch.cab">
      <PatchBaseline Id="PATCH"/>
    </Media>
    <PatchFamilyRef Id="MainPatchFamily32"/>
  </Patch>
  <Fragment>

    <PatchFamily Id='MainPatchFamily32' Version='1.0.0.0' Supersede='yes'>
      <ComponentRef Id="***"/>

Thanks in advance.



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