Snow Leopard changing files and folders to aliases

At random times, Snow Leopard is changing random files and folders to aliases that point to nothing. The original file or folder is lost! This is a very, very serious flaw in the operating system. For the four files I've lost this way, I was able to restore them with Time Machine. I only noticed these files were lost by chance. What will happen to those that I haven't noticed? When my Time Machine partition becomes full and it starts eliminating older versions, those that I haven't noticed will be gone forever. A file system is supposed to preserve my data for me; I shouldn't have to worry about it. And I shouldn't have to rely on Time Machine for flaws in the file management system. This is very, very bad! It is not possible to overstate how very bad this is. Has anyone else noticed this? Does Apple know about this? Is there a known cause? Is there a known fix?
Message was edited by: required desired alias

I haven't looked at any console logs. I'll have to figure out how to do that. I suppose I have to do it soon after I discover that a file has been altered.
It has happened to my data files in the data partition.
There are lots of good reasons for separating the system and applications from my data. It makes backup management easier. My data I want to backup frequently. I don't want to backup the system very frequently. If the system develops a bug, I don't want a backup of the system to overwrite a good old system in my backup drive before I discover the bug. A separate partition for my data makes backups of my data faster. There are thousands of files down there in the system and with everything in a single partition even incremental backups (via SuperDuper) take a long time to scan through all that system junk to find differences. I don't like to have to drill down three levels in the file hierarchy to find my stuff in the user folder. My data partition sits on the desktop as it did in systems 5, 6, 7, 8, and 9. If I keep my data in a separate partition, I can do anything that I want with the access permissions for my data. (Don't ever mess with the permissions in the system partition; it can really screw things up.) I can set the permissions so that I don't have any problems when accessing my data from another computer or as another user. Systems break occasionally and it's easy to restore just the system and applications from a backup of just that. I never have to go back to the install disc; if you restore from an install disc, you have to download and install all of the system updates posted since your install disc was printed, you might have to reinstall applications, you have to find all of your registration numbers for your applications, you lose all of your preferences. I also sometimes run multiple systems. I never buy into a new system right away. I keep both the new system and my old system in separate partitions while I try out the new one. If I find unacceptable bugs or limitations in the new system, it's easy to switch back to the old. If I find I've got an application that has been rendered obsolete by the new system, I can easily switch back to the old system. I mirror my data partition to my laptop. The system can't be mirrored to another computer and all that I want over there is the stuff on my data partition anyway. Mirroring the data is simple when it is all collected in a separate partition in both my desktop and my laptop.
I'm passionate about partitioning. In the Mac I just retired, I had 4 physical drives, but I repartitioned them creating RAID arrays (for speed) such that each of the 4 virtual partitions (system, data, scratch, & backup system) did not correspond to any physical drive. It worked fine for years.

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