Sounds really weird.

But Sikuli does not have any kind of "memory",that can lead to such
things in different script runs.

BTW: how can you be sure, that Sikuli finds what you think it should
find in that "failing" moment?

May be it finds something similar, because the one it should see is not
yet ready.

Logging: the easiest is the highlight() feature, because it shows the
red frame on the screen and prints a log with position and score of the
match.

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https://bugs.launchpad.net/bugs/1211462

Title:
  Image similarity value changes randomly

Status in Sikuli:
  Opinion

Bug description:
  When images are first captured, they have a similarity value of 1.0,
  and match exactly. However, when a script is run later, the similarity
  value for images degrades, typically to a value of ~.6, despite the
  exact same screen being visible. It occurs seemingly at random;
  typically it takes several days before an image will no longer be
  recognized, but it can occur faster as well. Because of the random
  nature of the error, it is difficult to reproduce intentionally, but
  seems to occur very frequently when scripts are tested at a later date
  or on a different client machine.

  Sikuli: 1.0.0
  OS: Windows 7 32-bit

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