UI double buttons

[Cuky]

Since 1.1 I have a problem where UI buttons for some of the mods are shown twice, while only one of them works. It started with Kerbal Alarm Clock and since it still isn't officially released for 1.1 I thought it may be the problem with the mod so I deleted KAC. Since then I have MechJeb button shown twice at the bottom of the screen in VAB/SPH and Scan Sat button shown twice durign flight. In flight sometimes both buttons are shown next to another one, while sometimes there is Docking Port Alignment Indicator button in between

 

Here you can find log from when I last played today

 

And 4 pictures showing what I get:

Edited April 24, 2016 by Cuky
Added screenshots