Weird, I just had an issue with it as well. I've been re-doing my site and tried the plug-in for the first time a few days ago (very good plugin by the way!).
Anyway, this morning I noticed it wasn't working. I figured I'd added something that made it quit. Then I decided that maybe it was because I moved my files from the sub-domain I'd been testing on and maybe it needed to be re-authorized or whatever through flickr, so I went through that process again and did notice that the website set up on the flickr app needed to be updated to match my main site.
Still no dice, so I tried changing themes to the standard 2010 theme. Still no dice. I had tried turning off a couple of plugins to no avail and finally reading this thread turned them all off and then turned back on Flickr-gallery. Yes, it works! So, I figured some plugin was indeed to blame. The weird thing? I've just re-enabled every single one of them and it's still working?!?
Any clues? I'm kind of afraid that it will start not working again without me being aware.
A link to a page using it on my site if it help in the suggestions is:
The symptoms match this thread, the lightbox would start to load and then it would just fail and go straight to flickr. If you weren't watching you'd have missed that the lightbox even tried it was so quick.