The /PAE switch won't help. Windows XP can't see memory that is moved above 4 GB boundary, so however much "address space" (from 0.5 GB to 1.25 GB) is needed for peripherals is taken from that 4 GB range, and there is nothing to be done about it (except upgrade to a 64-bit operating system). Your motherboard, BIOS, and installed cards - especially video cards - determine how much of the "address space" is used up. If you see 2.99 GB now, that is all you are going to see. (That's what I see on my Core i5-750 which is running XP Professional, with 4 GB RAM installed.)
Don't sweat it -- you would not notice any difference in performance if you DID get to use all 4 GB.