I figured this out. For me, the script which replaced the “Tweets by @Keith_Irwin” link with the actually widget was not working because I was using it inside a jquery .load() element.
On my site I had my raw page content in a div element (so it would load first). After the content loads, a .load() function replaced it with another html doc (called frame.hrml) which contained all the CSS and header and navigation and formatting for all the pages on my site. On frame.html there was another .load() which put the original raw page content into the body element. Once that was done, the twitter script was somehow unable to replace the “Tweets by…” link with the widget.
I solved it by moving the to frame.html, right after the .load() loaded the raw content.
Not sure if this is general enough to help anyone… but if you used jquery’s .load() function, that might be the root of your problem!