Unfortunately, any content in a Reference frame is not carried over by the current Publish modules, regardless of whether or not it is an an AFrame.
With FM12, you have to change your layouts to ensure that any graphic you want to show up in the ePub or HTML outtput is in an AFrame and that means a lot of manual work. Either scripting or Silicon Prairie's AutoText (see Silicon Prairie - FrameMaker Products ) would be very useful for this.
If you can wait another year or so (if Adobe follows their typical release timelines), then perhaps the next version may have this behaviour addressed. With enough users complaining about this, perhaps a patch may improve this behaviour even sooner.