@skeets
Yep, that problem is builtin with findAll(): in some margin around a match 
another match will not be looked for (speed), which makes sense for non-solid 
images. If an image can be found more than once in a region, it is not 
predictable (due to the underlying OpenCV feature matchTemplate()) in what 
sequence they will be found.
For solid images these 2 effects together lead to your experience.
Even when looking for a solid image in a larger solid region, the match 
location is not predictable and might not be reproducible. 
There will be no change for that behaviour in version 1. 

I am not sure wether it changes the situation, but did you try with
Pattern(image).exact() instead of just image?

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https://bugs.launchpad.net/bugs/1409098

Title:
  findAll limited to 100 matches

Status in Sikuli:
  In Progress

Bug description:
  Calls to findAll seem to report at most 100 matches., silently
  discarding any further matches.  Suggest findAll be configurable to
  specify the maximum number of matches, even if the default is 100, in
  the same way that similarity defaults to 0.7 but can be configured.
  Also suggest that if the max is exceeded, an exception is thrown so
  that missing matches can be spotted easily

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