I have exactly the sane problem, even if Aperture is the foreground application.
According to the manual this means:
Yellow: All masters in the library have been backed up, but a change has occurred to at least one version (such as an adjustment) that has not been backed up. The vault should be updated to safeguard your work.
I have updated all 3 vaults multiple times and they remain yellow. Is there any way to correct this, or alternatively find out which picture creates this problem?