Emulator

Not reproducible.

I can reproduce this using Mamario's x86 build of 3.0-201 (a post-3.0 revision, so its hash shouldn't matter here) on Windows 7 x86. Oh, and the problem also seems to occur with the Wiimote configuration window, more specifically the button-mapping window.
Let me list the steps that should reproduce this problem:

1. Have Dolphin boot a GC or Wii game (apparently, any game will do);
2. Shortly after that, click the "GCPad" GUI button.

If done correctly, the renderer window's title will be stuck as "Clearing code cache" for a few seconds, as a result of the GUI hang (obviously). After that, the GCPad configuration window will show 8 tabs, numbered from "Pad 1" to "Pad 8". The last 4 pads look like duplicates of the first 4 ones; when the problem occurs they have the same settings, but they are distinct objects (so a change on a pad object won't affect its duplicate counterpart).

When the GCPad configuration window is closed (through "OK" or "Cancel" or the "X" button on the top right-hand corner), Dolphin will crash as soon as an "emulation frame/cycle" is performed. You can confirm this by:

A. Booting a game properly;
B. Activating the "Frame Stepping" feature (basically, the only way to pause the emulation from within the child window which takes all the focus);
C. Stopping the emulation;
D. Booting a game improperly (this time following steps 1 and 2);
E. Closing the GCPad configuration window;

(F. Reopening the GCPad config window which will now have 4 tabs instead of the previous 4)
(G. Closing the GCPad configuration window... again;)
H. Noticing how Dolphin doesn't crash upon closing that window, but rather upon pressing Play/Pause which executes a "frame".

Most likely a result of deleting Pad-related objects while the emulation thread still has pointers to those, or some other unexpected behaviour. Some debugging may be required though... (Feel free to get to it, not sure I am going to do so)

We'll reopen if it appears again.