New mail now goes straight to trash!

I've been using Mac Mail and .mac, mobileme and icloud for years. This past week (or more?) some/most but not all icloud mail seems to go straight to trash unread rather than inbox. This even happened (and alerted me to a problem) when I was looking out for mail while on the phone to sender, who eventually had to send it to me at gmail instead when we got tired of waiting for it to arrive. Otherwise I would not have investigated and found several pieces of missing recent mail!
Not all mail goes to trash, but I can't see any pattern; for instance, one mail (received) asked for feedback on a previous item (not received). This inconsistency is scary because you don't know what you might be missing without continually checking trash. Tempted to abandon icloud mail for the time being?
I have checked and confirmed that I have not changed any mail preference settings (behaviours and rules). This 'missing mail' phenomenon has been consistent across my mac (OSX-ML) and IOS6 devices.
Help?

Thanks so much for trying to help. I really appreciate it.
Yes, the list of folders appears to all be correct.
Trash says: move deleted to trash (check), store deleted on server (check) & perm erase when 1 month old.
All accounts have the same setting, except the pop but it is very close and it's not the one with the problem.

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