Hi all, I've the same problem.
Since the previous release of firmware (2.x) the startup time was fine, once installed the 3.1 in july the time increased drammatically (with 2500 books the startup taken 45 minutes!!!!!).
I've written to Cybook support and they sent me a link to a firmware version (3.0) that fix everithing but has no "cool" features listed in 3.1.
So I've reinitialized my device, remove books, check the memory device and defrag it, install 3.1, and copy books again via Calibre.
Now with 400 books only the startup takes more or less 4 minutes that is no 45 (but with less books) but is too much for an ebook reader.
I'm not a device expert what I could see is that with previous version (2.x) the manifest directory contains data that are no more present now and that the 3.0 bin file was 31 Mb whilst the 3.1 is 17 only.
I'm a little bit sad
