I think I narrowed down the problem to incompatibility with another plugin, External Links.
http://ww.wp.xz.cn/extend/plugins/sem-external-links/
I’ll take a look at that plug-in and see if I can see what’s up.
Thank you replying and checking, I disabled that External links plug-in and it works perfect now, if you have some time to figure it out it would be appreciated but if you don’t I understand.
Okay. It seems that the “external links” plug-in kills the normal JavaScript on threaded comments, even without my plug-in in place.
Just tried this plug-in on my dev environment with 2010 theme and just the external links plug-in. They still sort of work in the none JS way after throwing an error to the console. The problem shows itself more readily with my plug-in as there’s a load more javascript for it to break and I’m doing a fair few things to avoid page reloads.
Just done a little more digging and it seems the problem comes about as a result of the “external links” plug-in changing the quotes in the anchor tag from single quote to double. That conflicts with the double quotes that WordPress uses in the reply link’s javascript effectively closing off the JavaScript before it has really finished.
So onclick='return addComment.moveForm("comment-8", "8", "respond", "1346")' becomes onclick="return addComment.moveForm(" with the rest of the code looking like more attributes to most browsers.
I could strip off the WordPress onclick code and use my own method with relative easy by I’d suggest you contact the author of the external links plug-in and ask them to fix it as I’d only be masking someone else’s problem.
There is a simple fix for this. Go to External Links Settings and untick the box marked “apply globally”, post and comment content will still be dealt with but it won’t try and do every link on the page.
Thanks for looking into this, I will contact them but it was more of a convenience to my users so they did not have to navigate away from the site when links were posted, I removed it until they fix it.
Again thanks for your time and explanation.