Windows 7 - CHKDSK discovered free space marked as allocated in the volume bitmap.

chkdisk on my new Windows 7 install returned the following:

This is a brand new clean install of Windows that's barely been used. What could have caused this?

I'm trying to troubleshoot problems with slow boots and general lack of responsiveness, and have reinstalled three times now trying to fix it...

Have a look at Brink's tutorial explaining how to read the Event Viewer log relating to chkdsk, which may give you some pointers as to what's going on.

Check Disk (chkdsk) - Read Event Viewer Log

How big is your hard drive? Problems will manifest themselves if the drive is getting full.

It was a 1TB drive, but only one 100GB partition (for the purpose of 'short stroking'). Windows was only just installed, so there was barely any space used.

This is simply telling you that the MFT on the filesystem contained references to file blocks that should have been marked free, but weren't. Assuming that's all that it found, it isn't likely to be a major cause of system performance issues, so it might be beneficial to know exactly what other issues you are seeing as well. This could simply be a symptom of other more major issues.