Took me 10 hours to figure this bug out. If you need javascript interaction on linux you need to add a flashvar with the DOM-Id in it.
ie:
<param name="flashvars" value="id=player_id" />
Would be nice if this would be documented, or did i miss something?
The 4.3 version in /trunk/ is completed in terms of coding. You can use that one. If, in this version, you set the DOM ID with the 'id' flashvar, it'll work in Linux too.
Pity though that the automatic ID retrieval through ExternalInterface.objectID doesn't work on Linux...
Next time, you could ask. That might take 10 minutes instead of 10 hours.
The id flashvar is documented here: http://developer.longtailvideo.com/trac/wiki/FlashVars#API