I recently purchased 4 GB of RAM (2 x 2 GB modules) for a Mac Pro (8-core, early 2008), that runs 3 or 4 OS (Win, Linux and OS X) in out dev environment.
NB: I used the base OS X install to verify memory.
I initially installed the 2 new modules in Riser A/DIMM 2 and Riser B/DIMM 2, then new memory did not show up, total system memory 2 GB.
Then, I swapped the original 2 x 1 GB modules with the 2 GB modules, giving:
Riser A/DIMM 1: 2 GB
Riser B/DIMM 1: 2 GB
Riser A/DIMM 2: 1 GB
Riser B/DIMM 2: 1 GB
This gave me, 4 GB RAM in total.
So, I moved the 1 GB modules to DIMM 3, like this:
Riser A/DIMM 1: 2 GB
Riser B/DIMM 1: 2 GB
Riser A/DIMM 3: 1 GB
Riser B/DIMM 3: 1 GB
Bingo, 6 GB RAM.
Are the DIMM 2 sockets bad? Or am I missing something?
Below is the current System Profiler output, showing 6 GB of RAM:
Memory Slots:
ECC: Enabled
DIMM Riser B/DIMM 1:
Size: 2 GB
Type: DDR2 FB-DIMM
Speed: 800 MHz
Status: OK
Manufacturer: 0x802C
Part Number: 0x3138484632353637324A4438304545314434
Serial Number: 0xE04920F9
DIMM Riser B/DIMM 2:
Size: Empty
Type: Empty
Speed: Empty
Status: Empty
Manufacturer: Empty
Part Number: Empty
Serial Number: Empty
DIMM Riser A/DIMM 1:
Size: 2 GB
Type: DDR2 FB-DIMM
Speed: 800 MHz
Status: OK
Manufacturer: 0x802C
Part Number: 0x3138484632353637324A4438304545314434
Serial Number: 0xE04921EE
DIMM Riser A/DIMM 2:
Size: Empty
Type: Empty
Speed: Empty
Status: Empty
Manufacturer: Empty
Part Number: Empty
Serial Number: Empty
DIMM Riser B/DIMM 3:
Size: 1 GB
Type: DDR2 FB-DIMM
Speed: 800 MHz
Status: OK
Manufacturer: 0x80AD
Part Number: 0x48594D5035313241373243503844332D5335
Serial Number: 0x05049101
DIMM Riser B/DIMM 4:
Size: Empty
Type: Empty
Speed: Empty
Status: Empty
Manufacturer: Empty
Part Number: Empty
Serial Number: Empty
DIMM Riser A/DIMM 3:
Size: 1 GB
Type: DDR2 FB-DIMM
Speed: 800 MHz
Status: OK
Manufacturer: 0x80AD
Part Number: 0x48594D5035313241373243503844332D5335
Serial Number: 0x05049201
DIMM Riser A/DIMM 4:
Size: Empty
Type: Empty
Speed: Empty
Status: Empty
Manufacturer: Empty
Part Number: Empty
Serial Number: Empty
You need to follow the memory layout suggested on the side door, and the instructions in the manual that shipped with your Mac Pro. The memory layouts have changed significantly from the older 2007 model Mac Pros.
edit: link to the memory replacement manual for early 2008 Mac Pros
Here's the Mac Pro (early 2009) manual on installing RAM. It's more than just installing in pairs, so read carefully.