Dear Tom, I checked your figures in LyX and could verify your problem. It seems that imagemagick is culprit. I converted your eps files to pdf and included that in LyX. That was shown perfectly clipped. So you could consider switchin gto pdflatex, converting all your eps files by a script using epstopdf command from MiKTeX. That, ofcourse, will only be possible if you are not using pstricks.
Mukhtar
