Syncicate has this problem because it only enables system multitasking for a very brief moment when saving data to HDD. The delay is too short for the filesystem to actually record the buffered changes to the HDD, thus filesystem will be left in inconsistent state. With PFS this means that the save doesn't work at all (PFS reverts to older consistent state, without the saved files).
I once fixed this by making Syndicate delay much longer after writes (4-5 seconds instead of the insanely short delay).
I can't remember if the installer already did something silly, but IIRC it was quite crude.
