Cheers, gents. That works now.
@gameutopia - From what I can tell Dolphin doesn't use links in that format in 7.1. I'm new so I have no idea how it used to be, but for example, Top photos now link like http://yoursite.com/m/photos/browse/top etc. so I'm assuming that's not going to be an issue with the current version.
Edit: On second thoughts, it probably has more to do with the permalinks structure than the Dolphin version.
2nd Edit: Actually, I see the links that I think you're referring to and they're not actually to the root dir, they're to /modules/ like this: http://yoursite.com/modules/index.php?bx_photos_mode=top&r=photos%2Fhome%2F&status=approved&ownerStatus=Array&albumType=bx_photos&page={page}&per_page={per_page}
If it were an issue I might have to do it the other way and make all links to root 301 to index.php so there's only one version. But I would loath to need to resort to that.
Thanks again or your help.