Are you using resource.clipStartTime by any chance? Using clipStartTime ends up passing in the optional start time when calling ns.play() e.g.
var startTime:Number = 30;
ns.play(videoName, startTime, -1, true);
Unfortunately this literally resets the videos true timecode to begin showing ns.time as 0:00 instead of the startTime (0:30). This is not a bug but by design for generating a playlist (not OSMF specific). See the attached docs for more info.
If you are using clipStartTime remove it then manually seek to your startTime as soon as the stream has loaded. If you're already doing that then I'm not sure why but it sounds like it's implementing a clipStartTime regardless.
That's the first time I've even heard of resource.clipStartTime.
I'm using a MediaPlayer objects seek method to seek, and getting the time from the MediaPlayer objects currentTime property. I don't know the internal imlementation of what those methods and properties evaluate to(it may be they're doing as you say), but it still seems like a bug.
I've sidestepped the problem by seeking, then playing, playing, and then listening for a seek complete event(time will be wrong at this stage), and then seeking again, which seems to work, but I believe this is a pretty dodgy workaround..