Laptop battery went flat, and my laptop has been running slowly since?

I'm using a Lenovo Z580 and I always use it whilst charging, for performance and obviously I don't want to have to worry about battery, due to this, my battery has only gone flat about 3 times. Usually my boot times would be around the 46 second mark, which was nice and quick. A few days ago, I was using my laptop and only running CCleaner when my battery went flat, since then I have had much slower boot times, the laptop is slightly slower in general but the main difference is the boot time, which is now taking 1 - 2.5 minutes. I ran a chkdsk and I have done malware and virus scans, nothing has been found. What could be causing this issue? And how can I go about fixing it?