I have some problems with this too: I even use the "Set 
options..."  - Build-tab - "Options" . If I use "%N" in the 
line, it should keep the original extension in tact, but it 
kills it and adds the type even without the preceding ".".
No fun if you need the original files, not the files with 
the mime-type as extension.
Other than that, a nice tool.

Greetings,

Jelle