Is there anything I can do to minimise the possibilty of this happening?

Only if you are prepared to rely on help from the user's intelligence, which appears to be a problem here. Are you clearly telling them that they will receive an almost-immmediate e-mail confirming the order? If so, it becomes their responsibility (I'm speaking as a consumer here) to check their spam periodically and adjust mail filters as necessary.

Unless you're selling viagra online or confirming casino membership. If so, there is probably not much you can do.

Webmail providers such as Hotmail and Yahoo have a reputation for false positives with automatically generated messages.

There are ways around this but if the emails are being sent from a third party server with your address on them this may be getting interpreted as spoofing.

I am sure somebody versed in the deep mysteries of email will give you some detail in due course. As a quick fix I would suggest putting up a warning that all orders are sent a prompt automatic acknowledgement and if this isn't received to check the junk mail folder.

Yeah, I have a message telling users that they will be receiving an email soon and to check their junk mail.

I'm not sure if people don't read this, don't know how to check their spam folder or some other reason.

Urk, I just remembered. Some e-mail providers have a user option for at-source filtering, where things the provider identifies as spam get routed to a webmail spam folder-- or deleted on sight-- and never even reach the recipient's computer. I had to turn mine off long ago because they interpreted their own mail as spam. This is a problem when you have forgotten your password and ask them to e-mail you a reminder. IANMTU.

There are many (mostly free) email checkers on the web to check for spam characteristics. Sometimes it's only one that snags it. Hunt down a couple of them and run your source code through them, this often helps.

+1 to rocknbil's thought. Your mail program may not be including a plain text copy of the message. This is a big hot spot for many SPAM solutions.

Are you sure you are getting all the bounces when you send out emails? (they are not going to your Spam folder). There is nothing you can do if their mailbox is full (other than asking them to clean out their mailbox befor clicking the last OK).

Your DNS may need DomainKeys/Sender ID/SPF txt records added to identify more closely your sending server to your domain. See openspf.org [openspf.org] for more on that. Also ensure that your outbound mail servers have DNS 'Pointer' records associated to it's IP address.