can't get it to work either ... this must be somehow related to eclipse's project/file management ...
if you really want to code AS3 however, than FlexBuilder really is not your IDE of choice ...
personally, i use FlashDevelop for AS3, but it needs windows ... it's worth virtualizing though ... also, it does a very smart completion on any as files and it supports AS2 and AS3, works quite alright with MXML, and provides rudimentary support for HTML, CSS, XML and PHP ...
apart from that, there seems to be quite a good textmate plug in for as3 ... but i really don't know of anything decent for linux ...
well, there's always FDT, but i somehow don't like it, and in my eyes it is too expensive for the features provided, that i'd use ...