Unforunately not savy enough to offer a lot of technical details here... but here's the problem. Hopefully the example will make it clear enough:

Say I'm reading an article like: http://www.wizards.com/Magic/Magazin...tg/daily/td/58

When I click on any of the links to a display information on a card it works fine (and opens in a new window but not a new tab). But until I actually close the new window no links to different cards will work. It use to navigate the newly opened window to the new card.

Before the latest Chrome update this worked fine.

Anyone know if there was a setting change I'm missing with the update or something?

Welcome to ChromePlugins
What's the version of your Chrome?

3.0.195.21

try updating your Chrome and see whether you can reproduce the error

It smells of a feature, not a bug...

Yep..

"Unsafe JavaScript attempt to access frame with URL http://gatherer.wizards.com/Pages/Ca...lstrom%20Pulse from frame with URL http://www.wizards.com/Magic/Magazin...tg/daily/td/58. Domains, protocols and ports must match.
Unsafe JavaScript attempt to access frame with URL http://s7.addthis.com/static/r07/sh0...aily%2Ftd%2F58 from frame with URL http://www.wizards.com/Magic/Magazin...tg/daily/td/58. Domains, protocols and ports must match."

So it seems to be a security matter..

Hmm. Annoying.

Any ideas for a work around? Or just live with it?

I'm not sure.. A guess would be, that the developer has to change, so it does not link to subdomains from the main link.. but I'm not sure if this is the problem..

Perhaps report the issue at http://code.google.com/p/chromium/issues/list at see if it's intented or they can give feedback how the webmaster can fix it..