My guess is its because you have talk mapped to a button on your mouse. When you go into commander mode, your whole mouse gets unbound and you cant change the binds on it. You have to map voicecomm to an actual key on your keyboard to talk while commanding.
And make sure it's not one of the already pre-bound commander hotkeys (you know, the ones you browse the menus with). I've made that mistake so many times.... <!--emo&:angry:--><img src='http://www.unknownworlds.com/forums/html/emoticons/mad.gif' border='0' style='vertical-align:middle' alt='mad.gif'><!--endemo-->
WHen your in commander, keys are unbound and binded to commander hotkeys. So for example, if your voice comm was the A key "Just an example!" that would no longer be voice comm, it would be drop ammo packs. I'm afraid you need to choose a key that isn't on the commander hotkey list.
I myself have a hotkey that I use for voicecomm fighting in the field, but I use shift for voice comm as a commander because it won't interfere with my actions.
You could also take a look at this question I asked a while back. <a href='http://www.unknownworlds.com/forums/index.php?act=ST&f=1&t=44452&st=0&hl=' target='_blank'>binding voice to capslock</a>
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I myself have a hotkey that I use for voicecomm fighting in the field, but I use shift for voice comm as a commander because it won't interfere with my actions.