Hi there.
Right around the same time I purchased and used the ‘Auto-Mailer Add-on’ I started to hear from customers that they were not getting my store e-mails, welcome notices, order confirmations, etc. I found out that the messages are still going out fine but GMail (and possibly Yahoo and Hotmail) accounts are putting the messages into the SPAM folder.
What the auto-mailer does is just sends out a standard template message which basically asks if everything was okay with the order they received, and provides links to the products they purchased in case they would like to leave a product review. It will once a day send out anywhere between 15-25 messages to all the customers that had an order shipped one week before.
Shortly after customers were telling me that never receive order confirmations, shipping notices, etc… which I found they are getting put into the SPAM / Junk mail folder by GMAIL and such.
I checked and my domain is not appearing to be blacklisted.
[url=“http://www.ahbl.org/tools/lookup.php”]http://www.ahbl.org/tools/lookup.php[/url]
[url=“IP Blacklist Check | RBL Check - BlacklistMaster”]http://www.blacklistmaster.com/check[/url]
I am not sure if it is the small amount of bulk messages sent out caused this, or if people receiving the extra message (asking if everything was okay with the order and providing link to leave feedback) and just clicking a ‘This is Spam’ button or something.
As far as I can tell there is really no way to contact GMAIL to get them to stop putting my messages in the SPAM folder.
Does anything have any suggestions of what I can do? Should I get another domain name and sent e-mails through that or is there some way to integrate a E-mail service provider that is reputable that messages will not get blocked?
Thank you so much for any suggestions … I get daily messages from customers saying they have not received any order receipt/confirmation. Plus not to mention contacting a customers that uses gmail, yahoo, or hotmail is almost impossible unless they check their SPAM folder often. 
-Tim
I once had the same problem but that was after a move to another server. It turned out something was not correctly configured in my server and after this was fixed the problem was gone.
You could try asking your host if they know what's wrong. Or start sending out mail through smtp instead of using your own server (for example google apps).
This is really annoying for you, I wish I could do more and hope you can get this solved fast.
Another thing to check is your server IP. It could be on a spam list.
Have you correctly configured your SPF record?
Read this article, as it addresses many issues in regard to sending out emails: How to keep your board from getting blacklisted as a spammer. - vBulletin.org Forum
It doesn't matter that its related to vbulletin. The same principles apply.
Also see www.dmarc.org
What style of mailer are you using? SMTP, PHP Mailer or Sendmail?
You should be using SMTP with authentication.
You will also need to have your hosting profiver create a PTR record for your IP address that references your domain. Sites like Yahoo and Comcast will not accept email when they can't resolve a reverse-dns lookup of the IP address and have it point to the domain.
Auto-mailer does nothing that would cause this. More than likely it is because you are using PHP Mail and/or you don't have PTR record for your domain. An SPF record and a DomainKey record also help get through the spam filters. Do a Google search for info on these extensions to email.
Thank you very for the responses! 
I was using PHP Mail Function originally … But when I started seeing this problem come up I switched to the SMTP authentication method, however this did not help at all. And I am worried that no matter what I do, my store domain will continue to be spam to GMAIL.
The reason why I mentioned the Auto-Mailer add-on was I stared noticing this problem and getting the e-mails from customer a week or two after I purchased and enabled the Auto-Mailer. Unfortunately, with the auto-mailer I cannot tell it to send the ‘bulk mail’ through another e-mail address.
I did check my domain name, plus both IP addresses (199.102.229.177 & 199.102.229.178 - main) and it is not coming up on any blacklist. I just found the mxtoolbox.com site too which does good information lookup and my domain is free and clear there also on all the blacklists.
tbirnseth, on your message about the PTR record, I did check and the test showed:
[color=#008000]PTR Record Found![/color][color=#333333] [/color]199.102.229.178[color=#333333] [/color][color=#808080]resolves to[/color][color=#333333] server.jammaboards.com[/color]
However, in my server I use mail.jammaboards.com for regular unsecured mailing … and server.jammaboards.com is for secure mailing. My STMP was set to mail.jammaboards.com yet the PTR record is pointing at server.jammaboards.com …
Do you think this might be the reason why?
I just changed my store e-mail SMTP setting to server.jammaboards.com and check it that works.
Also on the SPF Record … I just ran a check and it comes up with:
[quote]
SPF record lookup and validation for: jammaboards.com
SPF records are primarily published in DNS as TXT records.
The TXT records found for your domain are:
v=spf1 ip4:199.102.229.177 a mx ptr include:bluehost.com ?all
SPF records should also be published in DNS as type SPF records.
No type SPF records found.
Checking to see if there is a valid SPF record.
Found v=spf1 record for jammaboards.com:
v=spf1 ip4:199.102.229.177 a mx ptr include:bluehost.com ?all
evaluating…
SPF record passed validation test with pySPF (Python SPF library)!
[/quote]
I find this strange as it is showing ‘Bluehost.com’ which was my old host provider…My new host is ServInt. The ip on the SPF record is mine on ServInt (199.102.229.177) but not sure why it is saying Bluehost.com. Maybe on ServInt support they can fix this for me.
Flow, I have never see the Google Apps thing for e-mails before. At first I thought it would just send out e-mails with a @gmail.com domain … however looking at it is looks like I could send out up to 500 e-mails a day (which I do not send out more than 80 - 100 per day)…and they would use my actual store domain. I will really have to look into this also!
Thank you again everyone…really good advice to get my problem solved!
-Tim
Your SPF records have not been updated.
Your DNS Zone says “Legit Email comes from Bluehost + IP = 199.102.229.177”, obviously you are sending from a different IP which leads to the junk mail block on your domain for the most part.
If you choose to do so, you can login as root via SSH and follow these steps;
How To Add DomainKeys and SPF Records on CPanel Servers | Sohail Riaz
J.
Normally a PTR record just lists the domain name versus the fully qualified domain name. But if you mail is being sent from mail.xx.com and a reverse-dns lookup of the ip returns 'server.xx.com' then that could be a problem also.
Jessie's point above is probably the most likely cause of your issue. Sending additional security info that is wrong is a sure-fire way to insure a flag gets raised.