the --same-- thing happens in Yahoo and Thunderbird...I have tracked it as far as packet routers 'assuming' what you wanted, but more often it has to do with spam filters vs spam 'generators' muddying up the readers. One way to identify the problem is to read through 'full headers', but even that is not complete.
I have had similar issues of delays and mis-routings, and to date there has been no definitive answer...just electrons doing their thang playing with ones and zeros! The controllers will never admit a problem until they are affected financially...even then maybe not!
About the only thing you can do is monitor spam folders religiously, and use third-party confirmers such as MSGTAG mentioned above.