There are a variety of things that could be affecting what you’re seeing. One really simple thing to make sure of is, make sure you are comparing data for date ranges *after* you made the filter changes (because GA doesn’t change data in profiles retroactively, only from the time you made the change forward). Other than that, you didn’t say what data you were seeing that was different between the profiles, but discrepancies in what you see in these profiles could be due to some other setting that’s different, such as the query parameters you’re stripping.

In any case, it appears you’ve solved your problem with a new profile, so I’d just stick with the one you know is working correctly…

The problem I was having was that a profile I had set up with an advanced custom filter (profile a) seemed to be recieving less traffic than my control profile (no filters). I was sure it should have the same (which matches you findings above). I eventually set up another identical profile (profile b) with the same filter on as a. This time it matched the control exactly for visits etc. I removed all filters from profile a and it is still getting less traffic?????? I can only assume that Google Analytics isn’t entirly free of bugs and errors.

Thanks for your help.
Paul