I often get an Error come up in PhpED when saving workspaces and projects, for the various ppw, dsk, etc. files.

Cannot create file "C:\Users\plugnplay\Documents\NuSphere PhpED\Projects\xxxxxx.ppw". The process cannot access the file because it is being used by another process.

I am more than prepared to believe it is my anti-virus causing the problem, except that this problem started occurring around about v9 (I think) and my ESET anti-virus is set to exclude all of the PhpED file types including the $WRK files and also the whole of the Projects directory. The Error still happens if I turn my anti-virus off, although I have seen some anti-virus do strange things even when turned off and with exclusions.

I don't get any other errors like this from any other applications; PhpED is the only one.

Sometimes I have to save multiple times before it will finally work. I've tried investigating open files using sysinternals and have never found anything opening the file other than PhpED.

Do any other people get these errors?

More than often AV do not allow you to disable anything or disable themselves. They _pretend_ they allowed and do not show messages/warnings but still do what they normally do with slightly different "default answers". At least that's the case with Kaspersky and Symantec.
Try to export settings, then completely uninstall AV and re-check. If this helps, report to AV maintainers.

Interestingly, since I've been using the v13 Beta of PhpED, this file locked error has not occurred even once.

AV rules are quite heuristic and are based on sum of "risks". They may work fine with beta, then fail with regular release. They don't recognize it's beta (because there is no special sign to distinguish it's beta), but they may record full track of where you downloaded the package from, how you installed it and so forth.
Try to work with their support and check what can be done to avoid AV snooping into each file save operation performed by an application.