I don't use Calibre, but I doubt this is a bug. It sounds more like it puts its index into cache the first time round, and then just reads it from cache from then on.

I know you have quite an extensive collection of ebooks, so I can imagine your index file would be quite large. Maybe you should consider installing Calibre onto your SSD drive instead of your other harddisk. IIRC you don't really install stuff onto your SSD, right? In this case, I'm guessing it would make a big difference.