I just ran into this issue after most recent Windows Update. After doing some research, I found out that Microsoft again (yeah, i know) botched their update which is causing Windows 7 to run chkdsk every time it boots up. To resolve this issue, just install Windows Update KB2823324
If you do not know how to unistall updates (works for any Windows Updates), follow the steps below:
1. Go to Control Panel > Windows Update
2. At the bottom left column, you will see Installed Updates link, click on it.
3. Search for KB2823324, you can put the term in search bar at the top
4. Click on the update and click Uninstall. You are done!
As usual, if you have any questions or comments, please post it below.