[da-anda]

I've just tested and I'm not seeing that. Played an MVC mkv file, set video type to SBS. Enabled 3D mode, seeking stayed in 3D mode. Enabled "Play as 2D" and seeking stayed in 2D mode.
Tried with omxplayer enabled and disabled. A debug log (wiki) may help.

Note: I don't have a 3D tv currently, so I'm debugging with "Support MVC" enabled and "Use Full HD HDMI modes for 3D" disabled. Without the latter I don't get an image on TV.
Does disabling "Use Full HD HDMI modes for 3D" change the behaviour?

I was using 0401 for this test, but "Use Full HD HDMI" didn't have any influence on this behavior. As soon as I seeked in a MVC file while watching it 2D it was switched into 3D mode again. I noticed though that this only happens with mmal - so using OMXplayer only worked as expected. Unfortunately the TV is in use atm so I could only do a very quick test - will get you a debug log tonight.

@popcornmix - here is a debug log http://pastebin.com/7Qh3wtNx
I started playback in 3D, did a seek, then switched to 2D mode and did several seeks. The odd thing with this testing round was that seeking worked as expected for the first 2 seeks in 2D mode, but on the last seek it switched back into 3D mode. Hope this helps.

PS: sorry for the log spam by the PVR addons - seems I missed to disable one that got auto enabled/installed