+++++++++++++++++++++Edited for brevity.

> In the Help menu go to "About Eclipse" then click on "CDT"
> icon this will show you your CDT version.

Eclipse C/C++ Development Tools - Mylyn Bridge
Version: 5.1.0.200909110608
Build id: 200909110608


> Is eclipse OK when you create a CDT project using eclipse
> (and not using CMake)?

I don't see an option for creating a CDT project, does it have another name 
(besides CDT?)

> Which generated files? .cproject, .project?

I'm opening the generated .project with Eclipse

I have tracked down the only location I can find the offending include path
The include directives are being done by way of a 
-ID:\SVN\trunk\MY_PROJECT\subdir\include which is found in a CMake generated 
file named flags.make which gets created in 
D:\SVN\trunk\MY_BUILD_DIR\My_PROJECT\subdir\CMakeFiles\subdir.dir

> Could you send us the corresponding set of CMakeLists.txt

That would be difficult because our project structure is relatively 
complicated, I'd have to include many files in the appropriate directory 
structure, and I'm not sure my company would allow it.

>
> If not may be you can reproduce the problem with a "minimal"
> project, then  you can send an archive of this minimal
> project on the list and we will try on our side in order to
> see what happen.
>

I've tried this, but I'm not having much luck, I'll spend some more time on it.
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