AtmelStudio 6.2 changes the ISP clock when I try to run a program
I think I figured out the solution. 

In the .proj file, ATMEL stores the setting as ISPClock, but they don't read it back as IspClock. They try to read it back as DebugWireClockDiv, but that never exists.

So just open the .cppproj file and search for the following, and add the  element to match your IspClock.

&lt;com_atmel_avrdbg_tool_atmelice&gt;
  &lt;ToolOptions&gt;
    &lt;InterfaceProperties&gt;
      &lt;IspClock&gt;50000&lt;/IspClock&gt;
      &lt;DebugWireClockDiv&gt;50000&lt;/DebugWireClockDiv&gt;
    &lt;/InterfaceProperties&gt;
    &lt;InterfaceName&gt;ISP&lt;/InterfaceName&gt;
  &lt;/ToolOptions&gt;