Further info.
I have tried to reproduce the 'not-auto-adding' issue and I can't. I moved ebooks within the same VM in which calibre is installed, from other VMs in the virtual network (ubuntu and unRAID) and from my desktop (also Win 7 64) connected to the virtual network through a hardware switch, and I can't reproduce it
Another issue, with calibre minimized to the system tray, it has crashed very often while doing all this auto adding tests, but it didn't crash a single time when minimized to the task bar
Are there any logs I can check?