Peter:
GAlaxy is looking for the FastQC executable at the following location (see last line of error message):
/opt/galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc
You wrote that the fastqc binary is somewhere in Galaxy's $PATH, but is it really in the above directory? If not, try moving the fastqc executable there (or create a symlink) and it should work.
Best, Klaus
galaxy-dev@lists.galaxyproject.org