something very strange, and similar to this has happened to me before.
what happened with me is i found out that the network had either put services that were too advanced for the network on, or they had misconfigured them.
to make a long story short, services were trying to set modes that the IRCD did not support, and defaulted to the mode m. this happened most often when chanserv tried setting mode h (helpop) for someone on the channel. for some odd reason when u send (many) ircd's a mode that they do not understand, they will assume you mean mode m, lol.
this is a bit of a long-shot, but it's a possibility. good luck