Interesting theory, but it may not be the case.
A friend of mine used the same version of haxe and swfmill and it works on his computer.
The only difference seems to be in the swf-file generated from (the same version of) swfmill related to fonts:
diff:
- <DefineFont3 objectID="17" isShiftJIS="0" isUnicode="0" isANSII="0" wideGlyphOffsets="1" italic="0" bold="0" language="0" name="VeraFont" ascent="0" descent="0" leading="0">
+ <DefineFont3 objectID="17" isShiftJIS="0" isUnicode="0" isANSII="0" wideGlyphOffsets="1" italic="0" bold="0" language="0" name="VeraFont" ascent="19010" descent="4830" leading="4100">
As you can see the ascent, descent and leading is zero in my case.
Maybe a lib used by swfmill differs? Maybe libfreetype or something like that?
I'm running an updated Ubuntu 12.10.