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The annotations show some lines as changed more recently than what a CVS>Search History shows. Also the first hundred or so lines have no annotations at at. See screen shots.
Created attachment 59928 [details] Missing annotations at beginning of files
Created attachment 59929 [details] Annotation shows line 744 was changed in version 1.69
Created attachment 59930 [details] But the CVS diff show no change occurred there in 1.69
The missing annotations issue is probably duplicate of issue 129121, which should be fixed in current daily builds. => reassigning to version control module for evaluation of the rest of the problems
After reading issue 129121, I noticed the pattern... My annotations are not wrong, they are just offset by the number of lines that are missing at the top. So it looks like the second half of my problem is indeed related to the first. I will mark this a duplicate of issue 129121 (if I can do that). I will reopen if I still see the problem in the latest dev build. *** This issue has been marked as a duplicate of 129121 ***