hi mark,
i am surprise that it's working on ubuntu 11.04 - kiku is not showing in the taskbar (a bug in compiz), but it's not affecting the recognition afaik.
as for your problem, kiku have an option to recognize only the words if, in your example, pd-extended is opened causing kiku to restart his engine (thus portaudio). that might be your problem (i cannot reproduce this problem here, ubuntu 10.10).
you change this behavior in Configuration: Dictionary: Match V2C (uncheck)
also you need to know that kiku is single word recognition. meaning if you speak a sentence it will output a single word (with a very bad score).
remove ~/.kiku folder to "reset" the installation.
pat