When ever I am doing build or clean build, I am getting following error:
An internal error occured during:"Searching for Markers"
Using Flash Builder 4.6 on Windows 7 with 8 GB RAM.
Have you tried Project > Clean...? I get internal build errors all the time and even odder errors where a half dozen or so images won't embed without removing the @Embed('') bits from the source property. Project > Clean... fixes it pretty much every time. The few times it hasn't, unfortunately, I've ended up having to reinstall Flash Builder, which is a royal pain.
EDIT: Woops. This may be what you were referring to with a "clean build". I was thinking it was a vanilla project you were trying to build that was failing. My mistake.