*See Update *
I just noticed that Eclipse has released Eclipse Helios SR2 (3.6.2). Also last week we released a bug fix release for Liferay IDE 1.2.1. Unfortunately I have just verified that the latest Eclipse release (3.6.2 and WTP 3.2.3) is not compatible with Liferay IDE 1.2.1 (as well as previous versions). If you upgrade to Helios SR2 there will be a new blocking issue introduced during publishing of projects (deployment) that will cause it to fail. There is no workaround that I know of at this time other than to use Plugins SDK deployment via "ant deploy" build.
This issue can be fixed but it wont be available until next week, Monday at the earliest. Sorry for the inconveince.
*Update* Version 1.2.2 has been released that contains a fix for the previous incompatibility.. So just "Check for updates..." to get the latest version.