Apologies for the delay in replying.
On the off-chance I'd missed something with my original installation, I tried copying all the files from my 7.3c CD on to my Amiga 1200's CF card. I then proceeded to copy any libs to the libs folder and also copied the H folder to the root of my system partition. This didn't resolve the issue.
Next, I asked a friend to send me a zip of the files from their 7.3c CD. I copied these files over and the file persisted.
In the end I've gone back to version 7.1. The single pixel brush works for me on that version.
I'm still baffled as to why I'm having issues with 7.3 on OS3.2.1 and OS3.2.2. It was fine on OS3.9.