Could you please send me temporary access to your WordPress so I could check there what is going on? Send it here on the forum via private message(click on my nick, in top-right corner you will find …
You’re correct, changing the Permalink settings to “Plain” will cause the Lightbox to work properly, with ?work={work-title} as the links and #a13lightbox-work-{work-ID} in the Lightbox.