So apparently its the Blip Size slider that does it. Setting it to anything lower than 100% makes gathermates blips get bigger and out of place. This seems to be an issue since at least 2009 so im guessing it cant be fixed?
"I can confirm this with GatherMate addon that puts gather nodes on the minimap. If you scale blips it scales the entire blip map from the center point, effectively moving blips to the wrong position."