Previously downloaded molecules do not appear in the list

iPad3,1_5.1.1

I had downloaded a few molecules on fw5.1, that disappeared from the molecule list after updating to 5.1.1.
When I try to re-download the molecules, I get a popup error:

FILE ALREADY EXISTS
This molecule has already been downloaded.

Yet , again, the molecule does not appear in the list.
(possible file permissions issue?)