Tried again today following the format /s suggestion and the fdisk /mbr suggestion without success... Same error showed up again.
But then I fooled around a little more and did some partition analysis. I put my copy
of PartitionMagic 5.0 for DOS to a new DOS partition (actually Windows 98 that I had
sys'ed). After some analysis I finally found out what was the problem: the HD geometry
being reported on the GCT is different than the HD geometry reported on my Laptop.
When I formatted the partition on the Laptop, the HD reported 843x240x63 because of the Laptop translation algorith for large drives, which I didn't have control of changing). Then, on the GCT, the HD geometry showed up as 754x255x63 (used maximum number of heads and sectors and changed cylinder numbers). Then, for some reason, DOS boots OK when you install it on one geometry and boot it up in the other, I guess it may be because it doesn't fill up the space on the disk that has a problem with the change in geometry, but I'm not sure. PartitionMagic asked if I wanted to fix the problem in the partition table, but it didn't work either.
Then, my last resort was to format the HD again in a different computer. I hooked it up to my Desktop using a 44-pin to 40-pin converter (luckly I had an old one laying around at home) and then was able to choose one of three geometries in the HD auto-detection BIOS screen - the same that matched the geometry seen at the GCT. After this everything was a breeze. Formatted the first partition, copied the drivers, the Win98 cabs, and booted it up at the GCT. Windows installed OK then (finally). It is up and running.
So, if you format your GCT HDs in a Laptop, and it doesn't work, here is my experience. Check the geometry reported in your Laptop and make sure it matches the geometry seen by the GCT. I assumed the large disk translation algorithms were the same, but they weren't...
I hope this helps someone in the future with HD boot problems...