It may well be that 4.6.0 includes 1.0.9 for the full install. I don't know the answer there. In my understanding, however, the upgrade version of a DNN release does not include or update any modules. I am curious, though, whether or not the same goes for providers such as FCKeditor. My operating assumption is that it did not. (Can anyone weigh in on this?)
In this case, this was an existing version that was upgraded to 4.6.0 using the upgrade release.
Regardless of whether 1.0.9 is already installed on the server (it may well be) this error *seems* to have nothing to do with it being already installed but more with a missing file in the install package.
If this error does come from 1.0.9 being already installed, then A little error clarification on the installer seems in order. This would suprise me as I have succesfully installed modules of the same version multiple times without error. (in troubleshooting, etc.)
Another note: To my knowledge, there isn't a dnn page analogous to the "Module Definitions" page that lists the installed versions of providers such as FCKeditor. I'd gather that the assembly itself may have a version number (which I can go dig out), but that may a bit obscure for a (non-programmer) end user.