Alt-Up and Shift-Up do the same thing. So changing your keys to do Ctrl-Alt instead of Ctrl-Shift won't fix anything.
I'm hesitant to change it so that an unfocused chat window does not accept the keystrokes, because for one, its a standard that EQ1 and WoW follow (among other games, I'm sure), and for two, I like it the way it is :P
However, I *can* change it so that it only works with a single meta-key, e.g. Shift-Up or Alt-Up will work, but Ctrl-Shift-Up, Alt-Shift-Up, etc. will not work. This should resolve your issue.
I'll put it into build 1800.