@BetterRed: I might be the person who said the problem went away. What I said:
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My experience: I recently had to rebuild my windows 7 Pro/x64 computer. After all the updates etc were installed, calibre took forever to start, sometimes causing the entire computer to become non-responsive for 30 to 60 seconds. The solution: tell Windows Security Essentials to ignore calibre.exe. As soon as I did that the problem went away.
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I note that what I said isn't what I actually did. Instead of telling MSE to ignore calibre.exe I told it to ignore the entire tree /Program Files/Calibre2 as shown in the attached screen capture.
For me, no matter how long I waited after a reboot (I once waited 90 minutes), the first startup was horrible. My suspicion is that the problem comes from MSE scanning the pylib.zip file perhaps more than once. The improvement could come from it keeping track of what it scanned so it happens only once. As I said, after the above change calibre went back to starting lickety split.