I know I had purchased Bit.Trip RUNNER before... it was in in the Indie Bundle 6. I had problems running it on my Macbook Air, so I was wondering if they had a new version to fix the performance issues (it would go very laggy).

So I looked at My Library, and the title was missing. I also looked up the Indie Bundle 6 purchase page and it is missing.

So the only conclusion I can come to is that they are deleting titles from your library after you purchased them.