I have both a Kyser and a Shubb.
I tend to use the Shubb with my Stratocaster (are we allowed to talk about that here?) and the Kyser on my L-03-E.
I think I discovered a 'secret' for keeping intonation as good as possible on both guitars, but someone else probably has already talked about this at length.
What would cause intonation issues when capoing? Well, it's string tension. I tried putting the capo all along the fret and I get the best results when the rubber pad is actually resting a little bit right on the fret wire. This is true with both capos on both guitars. It's just enough tension on the strings to fret them, but not enough to put them out of tune like when you put the capo somewhere in the middle of the fret, or just behind the fretwire.
-Scott
That's what I do with my Kyser as well.
I like my Kyser except on certain chords (like F or 1st position B7) it gets in the way. Any suggestions for a good low-profile capo?