The reason your mob farm in the overworld stops working is because the chunks aren't loaded, therefore the farm won't be functioning. The workaround for this is to make a chunkloader and load the chunks the mob farm is in. As for the glitch I have no idea, I have noticed that as a common thing that happens in modded minecraft and personally I have just written it off as something you gotta deal with. For me tho, logging off and back on again tends to fix the glitches where things don't load and seem to just be a big hole in the world.