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Lohtse,
Where are the 44,000 ebooks that you want to add located?
It is possible that hardware configuration might be an issue. Calibre doesn't work well with network attached storage (NAS) or mapped drives, for instance. Some internet/cloud storage is problematic as well (Google Drive). And any HDD can have bad sectors or be failing.
Although less critical, have the source and destination drives been defragged recently? (Perhaps lots of drive head movement is causing delays which, added to other factors, is making things appear worse.)
I would also strongly urge adding books in much smaller groups. Start with 1 and then increase from there (5, 25, 50 , etc). Personally I would max out at adding 500 books or less at a time. I know you said you've tried several times and amounts, just not sure how small you went.
Unless you're using a "vanilla" install of calibre, it can be a bit difficult to get things arranged how you need/want them. The program's steep learning curve can also make things tough for new users. Once over those humps though, no other product comes anywhere close to calibre's functionality or feature set.
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