Maybe you are running some EVIL hack on your computer, such as Executive or MCP or whatever... and this hack is somehow interfering with or slowing down the write cache so that instead of it being written out in 3 secs it gets written out in 30 secs. Perhaps some evil prog is generating some enforcer hits to nonexistent memory or who knows what, and it slows your PFS down.
Lots of people have told me about the disappearing files problem on PFS and the disappearing dirs problem on SFS. Yet other people such as Piru swear that PFS is 100% reliable. So there must be something different between your system and Piru's to cause this problem.
Never underestimate the ability of reckless users to
not wait at least five seconds after a write before rebooting or turning off their Amiga. It happens all the time.
In any event, there is at least one hack that causes problems similar to this no matter how long you wait; DiskSafe. Version 1.14 of DiskSafe causes copies involving many files at a time to fail silently without setting a return code. This happens with the shell copy command and with copies done by Installer. I don't recall if using Workbench to drag a drawer from one partition to another also failed, and I never tested multiple deletes. This was discovered on an A3000 using AmigaOS 3.1 and FFS.