I was packaging the schema config files for IIS using the appHostSchema provider which included my custom file. When the package was created, my custom file wasn't included. This was also occuring when I was synching server to server, rather than using a package to see if that would make a difference. Again, my custom file was being excluded from the synch. This was working fine a couple of weeks ago.
Eventually I found out why this was occuring, I had recently put my custom file in source control which meant the file had become read-only. I manually copied the file to the config\schema folder on my local pc. When I tried to packing the files on my pc, it was now being excluded.
Once I turned off the read only setting, my file was once again included when synching.
