I was reminded of this recently when I read it on Ted Patrick's blog. To be fair, I think I first heard about this from Paul Thiel... but.. uh.. forgot. . .
In Eclipse, be sure to close projects that aren't currently active. Go to your navigator, right-click on a project folder, and select "Close Project".
It turns out that Flex Builder will scan all open projects & decider whether anything requires compilation. This will bog eclipse on open -and on save!