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Calibre database problem

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My system is a
  • Kobo Glo with
  • KSM 07(update02)
  • Koreader 2014.11-154
  • vlasovsoft 2015.03
  • Nickel 3.8.0
  • dual-booting Android
  • Calibre 1.48
  • Win XP SP3
My library is on the SD card inside a "/.Books/" (system) folder.
There are also two '/Books/" folders with a few more books if I need to read something in Nickel.

The problem:
Calibre does not update the 'metadata.calibre' database on SD card and on board.

I can connect the reader to the PC in 4 ways:
  • With KSM normally
  • With KSM using the Nickel ID
  • With Nickel
  • With Android
The only way that Calibre finds the books in /.Books/ is with Android.

With the 3 other ways a got the same results.
If the database is created (with the Android way) Calibre can see the books in the reader (can read the database and the addresses).
But if I add a book from explorer and reopen Calibre, it doesn't update the database. It can not see the book in the /.Books/ folder.
If I delete the database files, it finds only the books in the "/Books/" directories but not in the "/.Books/".
I tried with the 'Kobo Touch' driver and 'Kobo Touch Extended'.
The settings are the same on both, and since I don't use kepubs I can use either of them.

I'm certain that there is an obvious thing that I'm missing, but I can't find it.

Update: To make things even more interesting ...
Just when I was finishing the post, I tried to check if it can send the books into the SD card, so I reconnected the reader.
After countless tries with restarts and reboots, changing everything that I could think off, Calibre can not connect anymore to the reader with anything except Android.

It gives me this error:
Code:

calibre, version 1.48.0
ERROR: Error: Error communicating with device

database disk image is malformed

Traceback (most recent call last):
  File "site-packages\calibre\gui2\device.py", line 86, in run
  File "site-packages\calibre\gui2\device.py", line 490, in _books
  File "site-packages\calibre\devices\kobo\driver.py", line 1767, in books
DatabaseError: database disk image is malformed

I tried with a working set of database files (working just 10 minutes ago) and with everything cleared(no Calibre files at both roots).
I can see the reader in the PC just fine.
The only thing I did before was to try to search in the database with Koreader, which worked OK.
I don't think its relevant, but just stating the events.

Anyway, its getting really late.
I give up for today...

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