Ok, guys, I put you in the right direction!
With a file/folder compare utility I found that folders "editor" are the same both in WA version and in original FCKeditor one: so the problem should be somewhere else
I noticed the code generated by WA version and original FCKeditor: in the WA version there's this line:
<input type="hidden" id="EDITOR___Config" value="CustomConfigurationsPath=../custom/editor_EDITOR1.js" style="display:none" />
While in FCKeditor the same line is:
<input type="hidden" id="FCKeditor1___Config" value="" style="display:none" />
Guess what? If I remove the "value" string (<input type="hidden" id="EDITOR___Config" value="" style="display:none" />) the fonts are magically fixed!
So it's something related to the generated custom file, maybe some wrong path: can you check, please?