This behavior is consitent with all three "Free" fonts (Free Mono, FreeSans and FreeSerif). Other fonts that also come in different styles (e.g. Sans or Courier) can be set as expected.
This could be construed either as a problem with the TTF files or with Pango.
Line 756 onwards of pango/fonts.c (http://cvs.gnome.org/viewcvs/pango/pango/fonts.c?view=annotate) provides a list of common synonyms for various styles of fonts which are used by pango_font_description_from_string(). Neither "Regular" nor "BoldOblique" are in the list, which is why they can't be set. ("Normal" is down a bit on line 811, in case you're wondering.)
Inkscape makes the problem obvious because when you click Apply it sets the font then immediately re-reads the style it set in order to update the dialog box. I wouldn't be surprised if other applications using Pango exhibited some variation on the same problem on their canvas, even if the standard GTK font chooser didn't update to show the incorrectness.
My favoured solution would be both to fix the TTFs so that they use more standard names and to add the nonstandard names to Pango. Hopefully that way the problem would get fixed as quickly as possible for as many people as possible.
Richard.