when you first plug it in, you're supposed to let the RO/DI unit run for an hour without using the 'good' water. i guess it gets the sediment in the filters flushed.
has anything recently died in your tank?
to get phosphate down, use RO/DI water and frequent water changes. i wouldn't do large water changes EVERY day but maybe every 2x a week. dont want to stress the fish and coral out too much.
well your amonia is coming up (according to your test kits) and your nitrite and nitrate are 0. so im wondering if something happened to cause your amonia to come up and tank is started to cycle again.
your phospate needs to be as close to 0 as possible. so 0.25 is still relatively high...
i went to my local PetCo and could not find the limestone cube. am trying a regualr air stone right now. BUT as others have mentioned, would prefer to modify my biocube and install a better protein skimmer