I'm very sorry to hear about your predicament and I extend my full sympathies. This is just another example of UC Berkeley being the bureacratic mess that it is. But like all other things, going to Berkeley has its pains and its pleasures. The upside...you get to benefit from studying under some of the most accomplished professors on Earth and we have many Nobel Prize Winners, Pulitzer Prize Winners, Guggenheim Fellows, MacArthur Fellows, members of the National Academy of the Sciences, etc. The downside...the administration is a bureacratic nightmare and they occasionally lose important documents which studnents need (i.e.: LORs)...Somtimes, this school does really piss me off and reading your post just exacerbated that. You have my best wishes for a successful application process.