I receive this error whenever I run my extraction from the command line, not in the Spoon UI.
Missing plugins found while loading a transformation
Step : Mo
Just edit spoon.sh and add
OPT="$OPT -DKETTLE_PLUGIN_BASE_FOLDERS=$BASEDIR/plugins"
right after the line where the OPT variable is set.
This is actually the solution from mattyb. Editing spoon.sh will fix the problem for good.
Another solution is to create a symbolic link in your ${KETTLE_HOME}/.kettle directory which points to the plugins folder.