<a href=showthread.php?s=&postid=14804799#post14804799 target=_blank>Originally posted</a> by noahm
One thing you may or may not have done is looked at long term flow issues. Plug all your returns except one at a time to help blow anything out, clean powerheads, and more importantly blow all the crud out from in/under/around the rockpile if you haven't already.
Looking at your pics, I can see that the rocks haven't moved. You may be very surprised at what has accumulated under them and inside their pores. I would do small sections at a time as you are going to open up some real dead spots and release who knows what. Get a powerhead and really blow out each rock and vacuum up anything under.
Not that that is the cause, but while you are looking for stuff, why not. As above, run carbon, check your RO/DI for 0 tds etc. etc.