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You might want to defragment the drive with calibre on it (c:?). The reason this might help is that the calibre program is made around 1000 small files + some number of larger ones. When you start calibre, it must open all of these. If they have become spread all over your disk, then starting calibre could slow down significantly. Defragging your library could also help, although with the size of your library I wouldn't expect it to be a huge savings.
How much memory does your machine have? If it is small (less than 2 gb), then you should look at what is running at the same time. You might have installed something that runs in the background, consuming enough memory to force your machine to start using its virtual memory file, something that kills performance. Alternatively, you might have added a lot of data that some existing program uses. For example, Thunderbird memory use is quite sensitive to the size of the mailboxes.
As a diagnostic, before you start calibre, open the resource monitor and look at memory usage: CTRL-ALT-DEL, choose task manager, choose the performance tab, push the Resource Monitor button, then the memory tab. Let your machine run for a bit without calibre started, to get a baseline. Then start calibre and see what changes. Pay attention to the used physical memory and the hard faults graphs. If memory goes to full and the hard faults goes way up, then you are out of ram.
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