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I also have a 20D and make use of the 5fps more often than I should (I sure regret it at cull time!).
There's really no way that I can think of around the problem you've encountered since the shoot time is only recorded down to the second.
Personally I do the strict-filename thing with calvin's script. Neither solution is perfect of course, and I find myself violating my own naming scheme at times and breaking things. So is life.
Alessandro
P.S. If you make use of your 5fps with some frequency allow me to suggest you check out another script I wrote (I'm sorry I don't have a direct link but it's in the scripting corner) called Shoot Analyzer... I find it very helpful to oh well... I guess the name says it... analyze my shoots.
I try to avoid the high speed mode of my camera whenever possible, as I don't like culling many images. So I still shoot as if I am using film. But sometimes the 5 fps is indispensible. I used it three times in the last year, it highly depends on the objects you are shooting.
It is pitty that Canon does not use the sub-second field in EXIF, that would have solved this little problem. Maybe that field is used in their prof cameras (1D), I don't know.
I use a strict file naming convention as well, so maybe I can use Calvin's script. Being a new IMatch user I found that script quite daunting, and the simplicity of Ben's master-versioning philosophy appealed to me.
I just downloaded shoot analyzer, thanks for the suggestion!
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Enjoy!
Herman.