The first bug are you checking the VAS option when selecting the Ammo Box? without that you will not get Vas enabled.
OK the weather with JIP make sure you both have same MCC version and that he is in game before changing the time/weather.
Bug 3 I believe that that issue of removing zones has been added in the editor recently, but as usual check out the official MCC page or visit our website where one of the developers hangs out and uses his latest Dev branch of MCC.
see my signature for our place :) I hope this helps buddy.
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