The Doom 3 Version Checker is a utility program that you can use to help work out what is wrong with your installation.
You can download the checker from here. Once you have downloaded it simply extract both files from the ZIP, save them wherever you like and then run d3check.exe.
There is a dedicated section on the EMZ forum for assistance if you don't understand what the report means!
Please note that you need to have the Microsoft .NET Framework Version 2.0 installed.
An example report is shown below. In this case I have Doom 3 1.3.1 installed but I asked the tool to compare my install with the 1.3 Patch. It detects that the main EXE and gamecode PK4 files are installed in the right place, but are the wrong versions. It also shows that game00.pk4 and pak008.pk4 are from a different version and don't need to be there at all.