Are these opus files served by podigee? Podigee currently encodes their chapters as minutes:seconds:milliseconds instead of hours:minutes:seconds, like it should be according to the vorbis chapter spec.
Are the positions that AntennaPod displays in the chapter list offset? Or is it that AntennaPod seeks to an inexact position when trying to jump? Another thing that could cause issues is the fact that AntennaPod currently does not update podlove chapters after they are parsed for the first time. Could you try re-adding the feed (maybe just add a second copy with some random url parameters http://feed-url/feed.xml?xy) to see if the problem persists?