Same thing here.
The Mail From plugin will work only for the first blog in a multisite install.
I found a workaround.
Edit the plugin's file (mail-from.php) and go to line ~143. You will find the following code there:
<form method="post" action="<?php echo $_SERVER['PHP_SELF'] . '?page=' . basename(__FILE__); ?>&updated=true">
Replace it with the following:
<form method="post" action="<?php echo $_SERVER['REQUEST_URI']; ?>&updated=true">
You'll have to update the plugin's settings again but it seems to work now.