There's been no changes between 4.2.3 (the old version you mention) and the newest version (4.2.5) that should change anything with the Like button.
The site you mention is a completely different domain, which the bug on Facebook only affects specific domains. It's not known why certain domains are affected and others aren't, but that is the more likely reason why it may work on your other site and not the new. Other factors are that it seems to only be for 'new' content. Is the Like button working on the site you link to above with content that's been there a while, or is that for a new Like button?
Also, if you still have the 4.2.3 installation package, feel free to 'downgrade' your site that isn't working and let us know how that goes. If that does fix the problem, it will definitely help us narrow things down, but from the reports we've seen, users with multiple versions of JFBConnect are affected.. it's not just the latest v4.2.5.
Ultimately, if you haven't already, we'd highly, highly recommend using the "Does this repro describe your issue?" link on the Facebook bug report and noting that your site(s) are affected. Mentioning JFBConnect doesn't hurt as it allows them to know the different types of integration methods that are affected as well.
We are doing investigation on our side, but there's nothing we've found that we can do to fix this problem.
Thanks,
Alex