Thank you Antoine and Andrew for your quick responses. I'm not sure what's going on but GS/OS 6.0.4 is running much better now. But first I'll answer your questions.
Antione, my systems ran fine under 6.0.1 and 6.0.3. I never installed 6.0.2.
Andrew, I booting both systems from a 32 MB 2MG image I call System.HD from CF storage on the CFFA3000. My normal configuration is that the boot drive is on the CF and all other images are on the Thumbdrive. That makes it easy to add or change images on either machine. Both boot images are upgrades from 6.0.3 using the Live.Install.po included with 6.0.4 distribution image. I did some testing and both systems run fine from my 6.0.3 System.HD image. When I say opening and closing these volumes, I'm using the finder to open the drive images mounted on the desktop and opening and closing subdirectories or folders in their respective windows.
Yesterday I spent quite a bit of time troubleshooting this issue and I have more details and results. I noticed that when the 01 machine started losing access to the drives, the access LED on the Thumbdrive would blink for a long, long time and then stop with the OS reporting a damaged drive or asked to insert that volume. So I thought I'm going to move all the Thumbdrive images over to the internal CF. That was a lot of work as you know I had to tear open the machines, mount the CF and ThumbDrive drives in my Mac Pro and move gigabytes of data since each HFS image is 1.5 and 2 GBs in size and I have at least a dozen of them. Since I had the IIGSes torn open, I also backed up the storage which took time as well. I also scanned the storage under Win7 to confirm that the FAT32 formatting was good. It was.
I finished last night and recounted all the images on the CFFA3000 using only the CF. Both systems started working fine. I could open all the HFS partitions using the finder without any failures. But I still had a weird quirk with the 01 machine. On boot up, it kept reporting duplicate drives and wanted to relabel or eject them. What? That points to the CFFA3000 config file (CFFA.CFG).
Sure enough when I looked at the images assigned in the CFFA's smartport list, they were duplicated but I had removed all the assignments before adding new ones. I cleaned them out and that resolved that problem. For the 03 machine, it consistently reported one of the HFS volumes to be corrupted. I replaced that image from a backup and fixed that issue.
So I suspect that the CFFA.CFG files got corrupted even though that's never happened before to me and some images got corrupted which has never happened before either. So 6.0.4 appears to be working well on both machines. I reassigned two of the HFS images from the Thumbdrive to see if there were any more problems but, so far, no problems. I'll work on it when I have time.
To summarize, it appears to be a problem with the CFFA3000, either a corrupted CFG file and some damaged HFS images. My CFFA3000 firmware is 3.1 and I've noticed that on Dreher's website he as released 3.1.1. Maybe I should upgrade. I do have a 3rd CFFA3000 that's in my Platinum IIe but I have that in storage. I'll pull it if I have any further issues with either of these cards.
Thank you for taking the time to read this too long post. If there are any further questions, please let me know.
Gerry