Shadowbox stops working after ajax load

I had the exact same question as you. After much googling (and discovering I understand all of this much less well than I thought), I found this thread:

https://stackoverflow.com/questions/9144577/shadowbox-stops-working-after-jquery-function-call

So I tried pasting this into the “Reload Code” field of the Advanced Ajax Page Loader settings, and it seems to have worked:

Shadowbox.clearCache();
Shadowbox.setup();

I can’t claim to know if this is the best answer, but so far it is functioning for me. I hope this helps you, and anyone else who has the same problem.