Start up and shut down is slow after erasing free space using disk utility?

I went to Disk Utility, clicked Erase, and then "Erase Free Space." When I saw that it was going to take 1 hour and 30 minutes, I tried closing disk utility. It wouldn't let me exit, so instead I pressed "Skip." But when you hover over the "Skip" button it says, "Erase all data and reformat the disk."
I'm wondering if the fact that I pressed the skip button has anything to do with my computer shutting down/starting up A LOT slower now. If so, what can I do to fix it?
Thanks!

Just wanted to give an update. I called Apple and apparently, you shouldn't empty the free space using disk utility while you're logged in. I had to insert the Installations CD and press the "C" button while my computer restarted, and used Disk Utility from there. My start up and shut down speed still isn't exactly the way it was before, but this definitely made a difference.
Thank you to those who replied to my question!

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