Totally weird behaviour. Not consistent between sites. When I clicked on the toolbar button the NextGen popup, it didn't, it opened at the bottom of the edit page.
So I gave up, deleted all files except the wp-content folder and the config and .htaccess files, uploaded wp 2.71 again. Sweet. Then I try to auto-install TinyMCE Advanced, no-go needs at least 2.8! Ah ha, so I check it out on another installation, all working fine.
Back to the original site, auto update again to 2.8, install TinyMCE Advanced. Activate, test nextGen, OK, deactivate TinyMCE Advanced test nextGen still works. Reactivate TinyMCE Advanced, still OK.
Frontend? NextGen singlepics open 'loading' (thickbox) waiting waiting. Deactivate nextGen, reactivate. Thickbox popup now works perfectly.
So any answers? Nup. But worth persisting.