I fixed the problem on my phone (an S3). I discarded all of the "ghost" shortcuts from my home screen and replaced them from the All Apps menu. I rebooted and now the "ghost" SD-card icons only appear for a split second after boot.
I am having the same problem. I've cleared the cache and rebooted, and the problem persists. All of the icons for my SD-card apps are grey rectangles with the label "SD".
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