So, basically you mobo only supports 4 gig and due to board architecture some of the RAM is used for the system...hence only showing 3.5 gigs of usable RAM. Heres the quote.
Memory4 x240-pin DIMM, Max. 4 GB, DDR2 667/533/400 Non-ECC,Un-buffered Memory
Dual Channel memory architecture
* Due to general PC architecture, a small amount of memory is reserved for system usage and thus the actual memory size is less than the stated amount.