In the file tcomment.vimin your startup directory you should find the following list:
call tcomment
call tcomment
call tcomment
Here you will find this line:
call tcomment
Assuming you don't need to comment on Windows.ini files too often, you can simply change it to this:
call tcomment
Update:
This is a little better since you don't need to edit anything except your vimrc. Since your vimrc is usually loaded first, any built-in file types that we are trying to determine get overridden by the above file, so let's do it yourself:
au BufRead,BufNewFile, *.ini set filetype=pythonini
call tcomment
.ini , pythonini, tcomment.
vimrc , , tcomment, :
if exists('loaded_tcomment')
au BufRead,BufNewFile, *.ini set filetype=pythonini
call tcomment#DefineType('pythonini', '# %s' )
endif