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I've installed 2011.2.0.ca00bb7b3e88 built by Matthew Petroff (prebuilt_RC2)
The original project still has the same problem with Overviwe hidden. The original file is attached below.
And I've tried to start a new project with same photos. This time, I can't reproduce the error on that new project ! Both align and clean CP works normal.

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https://bugs.launchpad.net/bugs/813423

Title:
  Clean control points cause hugin not responding

Status in Hugin - Panorama Tools GUI:
  New

Bug description:
  After the first success alignment, I'm trying to use Clean control points in the image tab. but it always stuck and cause hugin to crash after one second. And the windows told me the software is not responding. I didn't experience that before. The CPU usage always stuck at 25%.
  Also, after all these, I'm trying to re-align my saved file. but it fail, too. The "Running assistance" windows works slower and slower and eventually stop (at least for 20 hours) at the same commend line. Also the Windows task manage told me the "autooptimiser.exe" stuck at 25%. I hit cancel, a window show up telling me the assistant did not run completely..... and automatically open the FPW and it crashs. If I manually force the hugin close, that autooptimizer.exe will still stuck there until I kill it via task manager.

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