Hi Jeremy!
Thanks again for your help looking into this. Apologies for disabling the broken functionality, I'll leave IS running this time so you can have a better look.
I've commented out the line involving relative urls - however this actually made things slightly worse. With that commented out, paginated blog pages also are having problems with the url changing (say, from '/blog/page/2' to simply '/blog'). With the line uncommented this effect is only seen on single post pages, not paginated blog pages too.
Thanks!