The default file naming script contains:

$if($ne(%albumartist%,),$num(%tracknumber%,2) ,)

This will produce a file name beginning in "00 " if %tracknumber% is empty.

I believe the desired functionality should be:

$if($ne(%tracknumber%,),$num(%tracknumber%,2) ,)

Also, think about entering the default script with some carriage returns and tabs to make it easier to read.