DB2 does have memory limitations for buffer pools on Windows 2000, but I am not sure if you are hitting the limit. For your configuration, you might want to use extended storage for buffer pools.
Also, check out the Administration Guide: Performance, page 266 where it discusses "Secondary buffer pools in extended memory on 32-bit platforms."
You might also look at APARs in fixpaks 3 and 4.
Using Windows 2003 Server with 64 bit DB2 will allow direct addressing of more memory.