Mails disappearing after MacOSX 10.8.4 update

Question

Following the update to MacOSX 10.8.4, all new emails incoming from any accounts (i.e. not iCloud only) are disappearing. This affects the Mac, iPhone, iPad, etc. With Mail app shutdown, mails are coming correctly (not disappearing) on the iDevices (I can't check on the Mac...).
Thank you a lot for your help.
Kind regards,
Charles

Answer 1

Thank you a lot! Disabling the rules is the solution (I can't tell whether Apple's Junk Filtering has an effect as mine is Intego's own set of rules (accordingly shown as a specific rule)).
This precise point should be further investigated if someone has the same problem and uses the built in Junk Filtering.
Here's what happened to the 200+ emails I received since yesterday (bad for zero inbox ). They all seem to have ended up in the Spam folder.
Re-building the mail boxes didn't have any effect (just mentioning, so that anyone who would read saves the time it takes...).
After disabling all rules, nothing seemed to have happened, but in actual fact all files started to show up in the Spam folder (it was empty before, I've checked numerous time).
Now, here's the strange point (to me at least): files started to appear account per account. First GMail (sorry guys... You know there has to be an account for all the junk newsletters ), then my personal domain, and eventually iCloud (possible reason: they were created in the reversed order (i.e. iCloud first)). But files from an account wouldn't appear before I moved those of the preceding account back to the Inbox (i.e. I first thought to have only recovered one account... The GMail, you understand my disappointment...). Accordingly, make sure to move the first files you find in the Spam, to see if something else isn't coming .
Voilà. Linc, Thank you again , you rock!
I hope this might help others with the same issue.