Yes, I did backup the entire device.
I did some reading and it turns out certain BIOS implementations simply can't deal with drives larger than 8GB. So now I'm trying to find a way to reduce the actual disk size as reported to the BIOS.
I'm sorry to dig up such an old thread, but I guess it's justified because the instrument isn't that young anymore either, and my problem is very similar to yours.
It is also possible that your CF card is not supported because it only reports it's size in LBAs, and not in the older CHS (Cylinders/Heads/Sectors). Many CF cards don't do this, because it is not mandatory for the CompactFlash standard. If the BIOS doesn't support LBA, it requires CHS, and hence the machine won't boot.
I too own an FSIQ3 with most of the HW options installed. I got it 6 years ago, and haven't used it very much, unfortunately. When I got it, I did upgraded the RAM: I got it to work with 2 SO-DIMMs of 512MiB each SDR133 RAM. I don't think 1GB PC133 SO-DIMMs were ever made, or are incredibly rare, expensive and unlikely to be supported.
My battery went dead, and because I'm a stickler, I wanted to replace it. Anybody knows how long it will last? Because it's a real journey to get to the battery. I ordered a new one. Tip: If you want one with the leads on it, order an LS14250
CNA.
I did not update the HDD when I got the unit, but I'm not waiting until the old Fujitsu MHK2060AT is breaking down. So now it's open, I'm replacing it with a Transcend TS8GPSD520 8GB SLC drive. It's industrial grade, according to Transcend. I hope it really is. I'm not concerned with speed. I'm more concerned with reliability: I have seen NAND flash memory fail in many devices. SLC is a good sign though. I hope my BIOS supports the drive.
After I have DD'ed my original drive to the new and bigger Transcend drive: Does anybody know if I can safely resize the partition so it will also span the extra size of the new drive?