For example, if the original boot.ini is:
[boot loader]
timeout=30
default=multi(0)disk(0)rdisk(0)partition(1)\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\WINDOWS
[operating systems]
multi(0)disk(0)rdisk(0)partition(1)\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\WINDOWS="Windows Server 2003, Enterprise" /noexecute=optout /fastdetect
You should add one more line with /3GB, i.e.
[boot loader]
timeout=30
default=multi(0)disk(0)rdisk(0)partition(1)\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\WINDOWS
[operating systems]
multi(0)disk(0)rdisk(0)partition(1)\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\WINDOWS="Windows Server 2003, Enterprise" /noexecute=optout /fastdetect
multi(0)disk(0)rdisk(0)partition(1)\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\WINDOWS="Windows Server 2003, Enterprise 3GB" /noexecute=optout /fastdetect /3GB