Hello,
I assume (but let me know if I’m wrong) that the start and end time values of annotations created on the Mac are still the same when opened on Windows, but that a different video frame is shown when e.g. activating an annotation?
If that is correct, the problem might be related to the encoding of the videos. On Mac and Windows ELAN uses different media frameworks and these might show different behaviour when e.g. jumping to a specific point in time. This issue is discussed in more detail in this thread and especially the last paragraph of point 1, about GOP and B-frames might be relevant.
But maybe my assumption is completely wrong.
-Han