Huh?
A 32 bit OS gives all processes 2 GB max, it doesn't limit your total RAM to that. The real limit is around 3.5 GB but it depends on hardware since things like PCI Cards and other devices can map into your memory address space.
To lose 1.5 GB is a whole lot, I must admit I've never seen that much... But if the bios is able to detect the whole 4 GB then I would look at what devices the system has, like sound cards and or graphics cards.
To read more on the /3GB or IncreaseUserVA options then I suggest you read the MSDN Article on the subject. This will NOT increase the total amount of memory the OS can access, if it was 3.5 GB before, it will continue to be 3.5 GB. All this will do is shift some of the memory above the 2 GB mark from kernel to user address space.