Books not appearing on Kindle

[sjw]

Hi,
Recently, on my Kindle Paperwhite, when I send books to the device they appear to go to the Kindle (and appear in the documents folder (as mobis)) - but don't actually show up on the Kindle when I try to see them.
I just added a .txt file, an epub and some mobis from Calibre to the Kindle - only the txt file appeared.
In the documents they are appearing as expected - folder with author name (surname, fist name) and in there is the mobi file and a folder of the same name with .sdr at the end.

Any ideas? Latest firmware and all indexed. (tried removing index folder too).

EDIT: Forgot to mention, if I email the same mobis to the Kindle they appear fine.

Thanks.