I know this doesnt help the situation, but I ALWAYS copy my whole mirc dir to another folder before updating in case of screw up during instal and Im recommending this to your users. once it's installed, if their settings are lost, they can just copy all the files back over and keep going.
Does that fix the problem? Nope, but it does give you guys a way around it for now until a reason and or fix can be found. Does it give them an error? Does it freeze at all during instal? Do they stop it during instal? More information (such as OS being used for example) would be needed to help find the cause.