I'm not 100% sure that this is a problem caused by BES, but it showed up soon after my email account was tied to a Blackberry, so this is my first guess.
I get my email from an Exchange server, but I connect to it from Thunderbird using IMAP. Everything mostly seems to work fine with this.
About the time that I got my Blackberry and had my email account enabled on the BES, I started to see a strange occurrence in Thunderbird. When I receive an email, it shows up in Thunderbird. Then it disappears. Then it shows up again. It usually disappears two or three times before it settles down.
I have tested this independently of Thunderbird by opening an IMAP session and IDLE-ing in my INBOX. It shows that Thunderbird is just doing what the Exchange IMAP server is telling it to do. Here is a log of the receipt of a single message:
. IDLE + IDLE accepted, awaiting DONE command. * 150 EXISTS * 4 RECENT * 151 EXISTS * 5 RECENT * 150 EXPUNGE * 151 EXISTS * 5 RECENT * 150 EXPUNGE
What that's saying is that it received a new message number 150 and out of those 150 emails, four haven't really been looked at. Then another "new" message appears (in reality, the same message again) as number 151. Then number 150 gets deleted. This makes the old 151 number 150. Then yet another new message appears, number 151. Then message 150 is deleted again. This takes a few seconds at most.
This happens for virtually every message I get and causes a lot of problems. It confuses new message notification, and I frequently get notification of "new" messages that are hours, days, or even weeks old. If I select an email and it goes through this process while it's selected, and then try to save an attachment, it can't find it until I deselect and reselect the email. If it happens to a message between the time I attach it to another email (or forward as attachment) and I send that email, the attachment fails.
I suspect that the problem is that my Blackberry is accessing the emails, causing BES to update something in the Exchange server, which then causes the Exchange server to recreate the email. I keep meaning to completely turn off my Blackberry and see if that keeps this from happening, but I have yet to remember.
(Honestly, my two preferable solutions are to get rid of the Blackberry and get rid of Exchange, but neither of those is going to happen.)