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Clearly some program/utility/service that is started during a normal boot is interfering with calibre. The primary suspects would be antivirus and security suites, but it could be something like a graphics or mouse driver. It could be some windows service. It could be some security setting. Or it could be some virus that sneaked onto your machine.
The approach I would take would be to disable startup programs one by one until the culprit is found. Actually, I might disable all of them (using msconfig), reboot, and see what happens. If calibre now works, then it was one of the disabled programs.Start them by hand one by one and try calibre until it breaks. Do a real reboot every now and then to verify that the behavior you are seeing is what will really happen after a restart. If calibre does not work with all startup programs disabled, then the problem is likely caused by some windows service or by something started by a service.
If this recently started, think back over what you might installed near when the problem started. If it installed anything that is started on boot, try disabling that.
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