There is no reason for you to have changed the automail.php script. I use the pop3 method to get our email and I did not have to make this change. We actually pull email from two different email servers and it works fine.
What you changed were variables that are pulled from the categories of eTicket. If you have different email accounts, then you need to create a different category for each so that eTicket knows it's to pull email from several accounts.
Line 120 to 124 on my automail.php looks like:
while ($cat_row = mysql_fetch_array($cat_res)) {
if ($cat_row['pophost']) {
$mbox = @imap_open('{'.$cat_row['pophost'].'/pop3}INBOX',$cat_row['popuser'],$cat_row['poppass']);
if (!$mbox) { $mbox = @imap_open('{'.$cat_row['pophost'].'/pop3/notls}INBOX',$cat_row['popuser'],$cat_row['poppass']); }
Yours should look this way too if you created a new category for each mail account.
Does that resolve the problem for you?