From this configuration you are running a 1st issue iSeries Intel 1366 triple channel processor?
The system will clock all memory the same so the 1600 will be clocked down.
The reported memory does not match the possibility that one DIMM has been missed. The only possibility is they are all dual banked (double sided) and only one bank has been detected.
Check the motherboard manual but you may have to run in Dual channel mode and use 2 and 4 for the 2GB and 1 for the 4GB.