Herman,
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.