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I could reproduce it now with the following scenario:
- I annotated a document in 'rotated-mode'
- Closed it and reopened in non-rotated mode => all is well
- Made some extra annotations in non-rotated mode
- Closed it and reopened in rotated-mode => all annotations displaced
- Closed and opened in non-rotated => all are OK again
- Rotated while document was open => all are stay OK
Note that I only used one page, I am not sure what happens on other pages.
So it seems related to annotating a document with different rotations.
Unfortunately the code for the 'native' PDF viewer and thus the annotating code is not publicly available, so I can not fix this.
Maybe you can work around this problem by being carefully with which rotation to annotate documents.
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