Volume setting not saved

Hello,
My volume settings are not saved when I power-cycle or reset my iMac. I have tried resetting the PRAM, with no effect. In another thread, someone asked me whether my PRAM battery might be getting old; the answer is, probably not, this computer was new as of this January.
One thing that's a little different from my other/previous Macs is that I have a Solid-State Disk (SSD) as startup disk and a standard Hard Drive (HD) for data storage. As recommended by various threads on the subject, to optimize performance while minimizing wear on the SSD, the /Users/xxx directory is on the SSD, but various sub-directories (Desktop, Documents, Downloads, ...) are on the HD. I've noticed that this leads to various odd perturbations (e.g. icons in the Finder sidebar only update when I click on them, can't launch a Parallels virtual machine by double-clicking its icon, ...), but I really don't see how it would be related to my volume settings.
Here's the machine configuration:
iMac (iMac11,3) 27" / 2.93 GHz Intel Core i7 / 16 GB RAM / 251 GB SSD / 2 TB HD
Mac OS X 10.6.8 (10K540)
Boot ROM version: IM112.0057.B00
Any help would be much appreciated!

Thanks for the suggestion. The Library folder is on the SSD, and I don't think the Public folder really has anything to do with this. But I did try moving the Desktop folder back to the SSD; the only thing that changed is that the Desktop icon in the Finder window sidebar is drawn correctly. The volume setting behavior is not changed.
I noticed something else, though: when I increase the volume and restart, the reboot chime is louder. This implies that my volume setting is correctly saved to PRAM, but then something else - during the start-up - cranks it back down. Does anyone have any suggestions on how to track this sort of thing?

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Volume setting not saved

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