Had to pop in just to say thank you!
I had the same issue. Sudden, unexplained crippling lag.
I first misdiagnosed the issue as running water. When starting quarries, I'd line the walls with source water blocks so it would create a lake instead of a gaping hole, and kill lava at the same time. Two birds with one stone right? Apparently not. Never thought that the water underneath the top row all the way to bedrock would be processed as running water. Installed worldedit to clear the top row so water would subside, which seemed to fix the lag. (3 quarries covering a 40x70 area)
Went about my business elsewhere and came back, same issue but no water! Was baffling.
After stumbling upon this post I went and (slowly) checked my chests, and one of them had hundreds of items spilled over it.
Needless to say buildcraft hates filled chests. Shame the items can't just move to the next in line, as I had 12 double chests lined up and the back 4 near-empty. That, and unloaded chunks where I found them spilled from the middle of pipes. I guess world anchors and teleport tethers don't work all that well either. I made sure all the piping/quarries/pumps were within the range of my 4 world anchors, and littered the pipeline with teleport tethers just to be sure using the F9 grid as a guide. Not much luck it seems though.
Just installed the NoLagg plugin to start stacking items that are floating around. That should (hopefully) eliminate the issue.
Thank you so much. Really.