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OK, I just figure it out about how to trigger this bug. I'll just describe how I'm doing this.
Hugin version:  2011.2.0.752ea80728d6 built by Matthew Petroff  (2011.2.0 rc3)
test with: 35 18-mm images. Some of the image are difficult to detect control points.

1.Under normal maneuver
 I load the images and directly hit align. A window pop up saying "2 unconnected image groups found: ...." I hit OK and hugin automatically junp to the control point tab and show one of each group. I go back to "Images" tab and select image 6 and 16,which I already know they are connected and CPFing can find CPs for them, and hit "Create control points" let the CPFind only concentrate on these two images. CPFind found 9 CPs. Back to the "assstant" tab, hit align again, assistant window show up and start running command lines. After it finished, the FPW opened and crash (with autooptimizer.exe at 25% of CPU usage). If you load lot more image at the first plase, it will just stuck at "strategy XX ...."

2.Bypass the bug
Load images, directly go to "images" tab, hit "Create control points" and let it find CPs. After finished, back to assistant tab, saying 2 unconnected image groups found:.... touch nothing directly back to "Images" tab,select image 6 and 16 and hit "Create control points". It generate 9 CPs. Back to "assistant" tab, it only remain "images are connected with XXX control points" hit align and everything runs smoothly afterwards.

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

Title:
  cpclean hangs on this specific pto file

Status in Hugin - Panorama Tools GUI:
  Confirmed

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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