Comment 27 for bug 772986

I was having this exact problem with my Matlab icon. It was working at the begining without a problem, until one day the icon became invisible.
I resetted the unity setting using:

gconftool-2 --recursive-unset /apps/compiz-1

After logging out and back in, I fixed my unity settings the way I wanted them and the icon was there again. I hope this can help anybody that is working on a fix to the problem.