this happened to me on one of the skins.I'm not sure but i think i just re uploaded either the shoutbox files or the style template files to overwrite what was already there.It sorted it out so try ajax first else the style one.
I doubt it is a problem directly connecting with converting from phpBB2 as the files are untouched on ModphpBB3 and the acidtech style. Try the above as john mentioned, or look within Paul's thread on phpBB.com on that shoutbox mod.
I actually prefer Handyman's Ajax version, and on styles I edit, I rid the extra chat link, and move the ajax version in place of that shoutbox.
To do that, open index_body.html for your style, find: