I had the same prob. turn off the heat simulation. It is right next to your username, left of "new page" (or just put a clone at the top of your water timer)
The problem was caused by rounding of particle coordinates, happening after checking whether movement is possible, and before actually doing the movement. This meant that the position moved to was not always the same as the checked position.
Some changes to the way that powder forms into piles caused this to happen more frequently in recent github versions. That allowed me to finally reproduce the bug consistently and (hopefully) fix it.