1. I had same issue. I turned off autoloot on all toons and activated Jamba´s Advanced Loot + autoclose lootwindow
2.try this:

/castsequence [nochanneling] spell1,spell2...

or

/stopmacro [channeling]
/castsequence ....

3. in ISBoxer you can add another step in your mapped key
http://isboxer.com/wiki/Step