File format passed to external editor

I could do with some help understanding how LR4 passes files to an external editor. My files in LR are RAW, and I am using both Photomatix and the Nik SW bundle. In the "External Editing Preferences" dialogue I have set the file format to TIFF.
To access Photomatix I go through the File>Export menu and it seems that TIFFs get exported. This makes sense to get key LR edits (esp camera profiles etc) burnt into the images that Photmatix sees, and to retain 16b resolution in the exported file. Is this correct? I can separately define the output (i.e. from Photomatix) file format in Photomatix itself.
Most of the Nik editors though are accessed through the Photo->Edit In menu though, and this pops up an additional "Specify Copy file" dialogue. I only get the option to pass the "Original with LR edits" as I'm working in RAW, this makes sense as above. I get an additional option to enter a copy file format of TIFF,PSD or JPEG though. Does this specify (a) the exported file format, (b) the file format to reimport, or (c) both? If (a) or (c) and I select (say) JPEG, it must be overriding the settings I have in "External Editing Preferences"..?
Many thanks, Steve

My problem is not the master file name but the random names. Lets say the original file name is _DSC0058 and I have done a rename of this project and the new file name is Jeanne 05. When I send it to CS3 it comes back Jeanne 006.
I am currently rebuilding my library because this problem is not happening in all projects.
Jeffrey

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