It's probably the same cause as with all those myriads of 4GB problems reported on this forum and on other pages:
The machine does not seem to support memory remapping. The fact that even the BIOS does not report more than approx. 3GB is a powerful hint here. To be completely sure, you might use a software from here http://www.geoffchappell.com/viewer.htm?doc=studies/windows/km/hal/api/x86bios/fwmemmap.htm
, which will indicate whether there exist memory regions above 4GB or not.
If they do NOT exist, then even a 64-bit OS cannot reveal the RAM regions hidden below hardware areas.
Checking with the Fujitsu download site, the latest bios version for this type of box is more than 4 years old, so I think you're out of luck here.
And I think it's highly improbable that Fujitsu will release a newer one. No matter how loud you cry...