Any chance you could provide specific steps that another person could follow independently to reproduce the issue?
For example, the basic steps for a simple web site might be the following:
1. Create a new web site.
2. Add a new resource file App_GlobalResources\Resource.resx with a string "String1" with value "Value1".
3. Add App_GlobalResources\Resource.fr-fr.resx with a string "String1" with value "Value1-fr"
4. Right click on the web site project, choose add Web Deployment Project.
5. Right click on the WDP, choose "Property Pages".
6. Select "Merge All Outputs to a Single Assembly".
7. Deploy output to server under IIS.
8. Request page default.aspx.
Another thing you could do is to try your web site deploying WITHOUT Web Deployment Project to see if it works.