I know next to nothing about MTS themes so why mIRC is rejecting it's settings I'm unsure, but I doubt it's a bug in mIRC.
Try setting the font manually with the /font command. So, if you want the Tahoma font with size 11, use:
/font -d 11 Tahoma
/font -s 11 Tahoma
If typed in the channel window, the first command will make all channels go to the Tahoma font with size 11, the second command makes the Status window go to this too. If you open a query and again, use the -d switch with the /font command all query windows should turn that font. See /help /font for more switches.
Hopefully, once you have typed this, then restart miRC properly (so use /quit and then close mIRC, or just type /exit), when you start it up again those fonts should be kept.
If you have further issues contact the author of the theme(s) and check out any documentation, as you may have not loaded something correctly or may not be loading it into mIRC correctly.
Hope this helps!
Regards,
