Theory:
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. If you figure out what is different then you will find the problem and permanently alter the course of Amiga history forever more.