Nathan,
I'm definitely using IMAP -- that's all I use so my mail is accessible no matter where I am. Also, all my other messages are on both computers and if the iPhone were set to POP some how, they would not have downloaded to the second machine, I'm pretty sure (unless I had told the iPhone somehow to keep the messages on the server which, as far as I can, see is not an option -- at least as currently configured).
The last time this happened I could not find the missing message anywhere on my laptop. This time I actually did find the message in my Trash on my laptop even though it was still in Inbox on my iPhone.
I don't know how often this is happening but I happened to catch it last night because last night I was traveling and some mail collected while I was on the road. My laptop was off and as soon as we arrived I took the dogs for a walk. While walking, I checked my mail on my iPhone and saw a message that needed a detailed reply. As soon as I got back home, I booted my laptop and the first thing I did was go looking for this message and I couldn't find it. If I hadn't been looking for it, would I have noticed it was missing? Maybe not, if I had already replied via the iPhone.
BTW, the unread messages before and after the message were retrieved by my laptop, just not the one I read.
Thoughts?
Chip