Firstly, if you don't understand text, go to 34:00 minutes into this video and it explains it.
Emit if empty conditional on storage block vs emit if empty with buildcraft - the emit if empty will emit if there is less then the amount the stroage block can output, but with conditionals it will only emit if the storage is completely empty. I am sure this bug in various other areas too.
I can't make a pipe signal effectively to convey that a block should stop a(say) reactor. This bug is really annoying and working around it is extremely annoying