As far as I know k63 ubiquitin chains usually (not always) induce protein activation. MG132 is a proteasom inhibitor, but the k63 linked proteins are not targeted to proteasom degradation. The ones linked with k48 chains are the ones targeted to proteasom degradation and there I will be expecting an increase after MG132 treatment.
Yes, I have a specific K63 antibody. Do you think that this decrease might be due to a overall effect, I mean, Total ub increases, in particular K48 (I suppose) at the expenses of K63? thanks ;)