A few months back I had a bad sector on my C drive and decided to replace it. After some consideration I decided on a 10,000rpm drive which started up roughly 30% faster as advertised, but now it is starting up Windows at the same speed as the old drive.
The drive has around 30% free space, has been defragged, and all AV etc scans show clean so why has this drive is the machine starting slowly?

How do you know it is the drive? Typically, if Windows starts slowly, it is because there is problem with a driver or some configuration problem, if not malware or spyware. the 10,000RPM drive should still be spinning at 10,000RPM and seeking and reading data at the same rates. It is what the computer and Windows does with it that matters. Or else you would be getting drive errors. Are you?

Many experts recommend no less than 30% free space. I think that is a worthless figure. There's a big difference between 30% of a 1Tb drive and a 80Gb drive.

Many factors affect Windows startup time - that does not mean something is wrong. It is how the machine runs after fully booted that really matters.