There are various issues related to quarries being reported. It doesn't go through water stream even after the stream is fixed, or reset itself after reload. See http://mod-buildcraft.com/forums/index.php?topic=13.0 and http://mod-buildcraft.com/forums/index.php?topic=112.0

i'll take a look at this if you want

Thanks!

i updated to forge .1039 and now the quarry doesn't reset anymore when you logout an login. The problem was that forges didn't save entity stuff properly causing the quarry to reset

fixed: #1495