Hi, we have two related problems here:
1) At http://www.lyx.org/trac/changeset/f496ec373bafa/lyxgit we changed the font style from "Regular" to "LyX" to work around a qt shortcoming. This is probably the reason why cmr10.ttf is not used any longer to display the superscript 3. Note that the discussion at the bug http://www.lyx.org/trac/ticket/9229 which was solved by this change did include the former maintainers of the Debian LyX package. We did try hard not to break any package depending on LyX fonts.
2) The font replacement algorithm used by matplotlib has a bug. It seems it uses some kind of symbol font which causes the omega instead of the superscript 3. This symbol does not come from the additionally queried cmex10.ttf font, I believe this font is tested because cmr10.ttf did not work, but is then discarded as well.
Georg
