Sorry to dredge up a rather old one, but I have a similar problem, and I am quite certain it's not pathing. I have a massive pile of sandbags right next to a large sand collection area.
Basically, I have a nice magma glass operation going. My whole economy is based on it. It worked perfectly for quite some time. Recently, however, it has begun to cause some problems. I couldn;t figure out why, but the game would momentarily slow to a snail's pace, then speed up to 100FPS again as it usually is. When I checked, I found this:
... ... hmm, well I can't figure out how to get pictures into forum posts, so I will just have to tell you.
I found that the reason it would slow down so much was because the system was spamming collect sand failures. "Dunat lilarnish, Farmer cancels Collect Sand: Job item lost or destroyed. x809" ... sometimes it's x300, sometimes x100, sometimes 1000+, but the announcement screen is filled with these reports, of collect sand cancellations. One of the wierd things is that, despite the high number of cancellations, all the glass furnaces I built (12) could only hold 120 total calls for sand, though they are supposed to be interspersed with 'make glass blocks' and such.