wix major upgrade not installing all files

I have a very simple WiX project (version 3.7) that installs somes files (a .NET program version 6.0.0.0). I'm ready to release a new version 6.0.1.0 using the MajorUpgrade functionality in WiX.

I'm keeping the UpgradeCode the same in the Product element and I change the Version from 6.0.0.0 to 6.0.1.0

<Product Id="*" Name="MyApp" Version="6.0.1.0" Manufacturer="Me" 
       UpgradeCode="$(var.TheUpgradeCodeGUID)">

On a machine with 6.0.0.0 installed, I run the new installer.

The removal of the old version 6.0.0.0 runs ok (all installed files are being removed), but when the installer continues to install the new version, 2 files are missing: a 3rd party DLL and a 3rd party EXE (that haven't been changed) are not being reinstalled.

<Component Id="AutomaticUpdaterWPF.dll" Guid="*">
        <File Id="AutomaticUpdaterWPF.dll" Source="AutomaticUpdaterWPF.dll" KeyPath="yes" Checksum="yes" />
</Component>
<Component Id="wyUpdaterProgram" Guid="*">
        <File Id="wyUpdaterProgram" Source="wyUpdate.exe" KeyPath="yes" Checksum="yes" />
</Component>

All other files in the < ComponentGroup > (some modified, some unmodified incl. other 3rd party DLLs) are being installed correctly during the major upgrade.

If I click on "repair" after the major upgrade, the 2 missing files re-appear. Also, if I install version 6.0.1.0 for the first time (no upgrade, but first installation on a clean machine), then those 2 files are installed directly and normally. (tested on several Windows machine (XP, 7 and 8)

Anybody any suggestion what is wrong and how to fix it?

The log file provided shows that newer versions of a few files already on the machine:

MSI (s) (0C:5C) [16:13:25:890]: Disallowing installation of component: {015A4DC1-56F4-562B-96B5-B3BE0D45FA5F} since the same component with higher versioned keyfile exists
MSI (s) (0C:5C) [16:13:25:890]: Disallowing installation of component: {4B6A1404-3892-5BEF-AB47-8FE3149211A4} since the same component with higher versioned keyfile exists

I've seen this problem with this updater in the past. Christopher is correct. The updater updated its files but didn't tell the MSI (it doesn't update the MSI which is not the correct thing to do). The new MSI thinks newer stuff is on the machine, chooses not to install its files, but during the upgrade the old package removes the files (it doesn't notice that the versions are newer). Since the new installer chose not to install the files you end up with nothing... until the repair.

To work around the problem, you need to move your RemoveExistingProducts action later. If you're using the MajorUpgrade element then Schedule='afterInstallExecute' or Schedule='afterInstallFinalize' should do the trick. You'll need to be more careful with the Component Rules.

Also, IMHO, the 3rd party vendor should not be updating files outside of the MSI. Their decision is forcing your product into a particular way of upgrading.

A log file would help. My guess is it's based on where you have scheduled RemoveExistingProducts. I've seen situations where Costing figures out a file being installed is the same as a file already installed and decides to not install the file. Then the major upgrade occurs and you end up not having the file. The repair works because the file isn't there and costing realizes that it needs to be installed.

I have had the same problem. The issue here is when doing major upgrade, msi at first checks which components to install (and all dlls with lower version than the ones already installed are marked as "do not install"), then it removes installed app and then installs new version but without those previously marked components.

Rescheduling of REP did not help since "disallowing installation (...)" was done in Costing phase and MajorUpgrade can only be scheduled in Install phase.

My solution was to set REINSTALLMODE property to "amus" in wxs file.

<Property Id="REINSTALLMODE" Value="amus" />

The "a" means all dlls will be reinstalled despite their versions.