This performance issue will not be found (nor solved) in your ISBoxer settings.
When you say "a few weeks ago", was this prior to the big WoW 5.0 patch? Since the patch there have been numerous reports of old WoW Addons causing performance problems, including Jamba
. If you use Jamba, make sure to get the new Jamba beta from THIS thread on dual-boxing.com: http://www.dual-boxing.com/threads/47757-Addon-Jamba-An-assistant-for-multiboxers-Patch-5-0-4-Beta-Testing-BETA-3-released
. If you're using the same version of Jamba you used before, or the normal download from Curse instead of the Jamba beta download, then it will be expected to cause performance problems.
To that end, it will be helpful to both of us if you go to your WoW Addons screen and disable everything but ISBoxer in order to see if your performance issue is caused by Addons.
Additionally, there have been reports of new performance issues under DirectX 11. Switching WoW to use DirectX 9 has been reported to solve some new performance issues since the 5.0 patch.