See Bug 377344 for more details This happens on: opensuse:tumbleweed:20170304 Qt: 5.7.1 KDE Frameworks: 5.31.0 KDE Plasma: 5.9.2 kwin 5.9.3 kmail2 5.4.2 akonadiserver 5.4.2 Kernel: 4.10.1-1-default
Still happens on with kmail 5.4.3 opensuse:tumbleweed:20170315 Qt: 5.7.1 KDE Frameworks: 5.31.0 KDE Plasma: 5.9.2 kwin 5.9.3 kmail2 5.4.3 akonadiserver 5.4.3 Kernel: 4.10.2-1-default Nouveau: 1.0.13_2.2
Closing this bug as it seems with my tests that its down to filters on incoming messages. If i uncheck the "Apply filter to incoming messages" on each filter and then just click on the inbox and click 'Folders/Apply all filters on Folder' to manually apply. I has so far not produced a duplicate email so its looking like filters on incoming is the culprit.