Thanks very much for your info. You're right... it works!
The only way, it seems, of using the EOS Utility properly (without resulting in file naming conflicts) is to set the option to NOT change the filename. Anything else seems to not be able to tell the difference between one body and another.
I really hate the original filenames, and don't care much for the Canon software either. I've got a naming convention that I've used for close to 10 years now and I'm real happy with it and I hate to change. I was hoping to have more flexibility in image naming with EOS Utility but alas, that's not the case.
What I'm doing now (thanks to your pointer) is having the images saved to both a memory card in the camera and the computer at the same time, using the original filename the camera sets. Afterwards I can use BreezeBrowser Pro to batch rename the images to the convention I use. Not quite as smooth as I'd like, but certainly I can live with it.
I've been using Chris Breeze's suite of programs for several years (BreezeBrowser Pro and DownloaderPro) and with them have developed a workflow that I'm really comfortable with. I always use the first three positions of the filename to identify the camera body used, followed by an underscore, followed by a sequential number. The filename in the camera might be "_P7X0123" but my system names it "p7x_00123". The Canon utilities don't allow me to do this.
I tested the trial version of Breeze's DSLR Remote Pro software and it has a really nice interface. In the live view mode there is a much nicer grid available than with EOS Utility's live view. And get this, it allows AUTOFOCUSING!!! (The Canon utility doesn't.) But unfortunately it doesn't offer the same flexibility of file naming that BBPro or DLPro offer and you cannot even maintain the filename that the camera chooses (and rename it later).
So right now the best option appears to be the EOS Utility, with the original filenames. Hopefully in the not too distant future, Chris Breeze will update his DSLR Remote Pro software to beat Canon's offering in that regard.
I'm not at my primary laptop right now, so I'm doing this from memory. I assume you are using the Canon supplied software (EOS Utility and DPP).
You need to go into the preferences of EOS Utility and there set the option to use the original file name. That's the name where there is a unique four character prefix and then a sequential number.
There is also an option to also record the image to the card as well as the computer.
If you want to send one format to the computer and keep the other on the memory card, set your camera to record the RAW to one card and a JPG to the other card. Then set the playback mode to playback from the card with the JPG. This is also the file sent to the computer when you are using a WFT.
I use this technique all the time. Give it a try setting it up and let me know if you have troubles.