I have the same problem on my Archlinux x86_64 install, running vanilla and extended with jackd. The same thing happens on my debian install on the same laptop (Core2 T6400, 2GHz, 2MB L2 cache, 4GB RAM). I don't live patch (yet), and found out that if you exit edit mode it works a little better (there's still the ocassional dropout).

It should be cleared that I run jackd with the same config for far heavier realtime dps stuff (many plugins loaded in ardour, with realtime input) and that I've already tried increasing the frames in jackd's config. The dropouts do not make jackd report an xrun, and here is my ~/.pdsettings

audioapi: 5 noaudioin: False audioindev1: 0 2 noaudioout: False audiooutdev1: 0 2 audiobuf: 100 rate: 48000 callback: 0 blocksize: 128 nomidiin: False midiindev1: 20 nomidiout: False midioutdev1: 65024 path1: /usr/local/lib/pd/extra/iemabs path2: /usr/local/lib/pd/extra path3: /home/fede/Documents/puredata path4: /usr/local/lib/pd/extra/zexy npath: 4 standardpath: 1 verbose: 0 loadlib1: iemlib1 loadlib2: iemlib2 loadlib3: iem_mp3 loadlib4: iem_t3_lib loadlib5: zexy nloadlib: 5 defeatrt: 0 flags: -rt -alsamidi -font-weight normal