Drupal 7 rewrite is removing get parameters from query string
It turns out that there was a bug in the latest release that in /modules/contrib/link/link.module that was causing the query strings to be stripped from the URL in the token. I replaced the code in this file with the code from the pre-upgrade version and it began behaving as expected again. This, of course, is not a resolution to the issue, but at least the source of the problem has been identified. For more info, see the original bug report.

I later found that there is a patch for this issue in the dev version (7.x-1.x-dev) of this module. Download this module and replace it in your install and you should be all set.