For quite some time I was facing a problem where Adobe Air applications particularly Tweetdeck (or any twitter client) did not open the links in my default system browser (Google Chrome) and opened the link in Firefox which was my earlier default browser.
Initially I tried to pinpoint the issue to Tweetdeck, but it seems like the issue is with Adobe Air itself.
This issue happens because even though you may have changed your default browser a registry entry pointing to the the .htm class type has not been updated by Windows. To read more about this issue visit Adobe Air / Firefox issue on Vista.
If your default browser is Firefox and the clicked links open in Internet Explorer, Adobe Air has included a fix in their release note, that will allow you to fix this issue. If your default browser is Google Chrome and the links are opening in some other browser, here is a fix that will point Adobe Air to open all links in Google Chrome.
There is also a more generic fix for opening Adobe Air links in any default browser.
Thanks to Iain Dodsworth the founder of TweetDeck for pointing this out.