I'm assuming that you upgraded the memory by installing a second set of DIMMs, bringing the total to 6 from 3 correct?
If this is the case, you will almost certainly need to bump the memory controller voltage and DRAM supply voltage up a bit.
Memory modules are organized into what are called "ranks". Each rank is a formed from a set of DRAM chips that when combined form a 64 bit data bus. Common examples are 4x 16 bit DRAM chips, and 8 x 8 bit DRAM chips. In terms of organization, all of the ranks on a memory channel share the same data and control busses. To prevent obvious conflicts, only one rank can be active at a time by virtue of a "chip select" which is unique to each rank.
Physically, ranks are organized onto DIMMs. Value memory modules often have only one rank per DIMM, but higher density desktop memory will often have one rank per side for a total of two ranks per DIMM. High density server modules will have two ranks per side, for a total of 4 ranks per DIMM. DDR3 supports 8 ranks per channel.
There is very little difference electrically between two DIMMs with one rank each, and one DIMM with two ranks.
Since each rank must be able to receive electrical signals on the chip select pins at all times (they cannot be disabled or set to high impedance using a tristate buffer), the electrical impedance on certain bus lines will decrease when the number of ranks increases. This reduces the signal quality with each added rank and increases the electrical load placed on the memory controller. Since enthusiast memory already operates with very little electrical overhead remaining, going from one DIMM per channel to two DIMMs per channel may push the memory outside of the bounds of stability for which it was rated. Most of the time this can be rectified by giving the memory controller and the memory modules a bit more juice to work with, which boosts the signal quality.
Another solution is to set the memory modules to use a 2T command rate rather than 1T. 1T is very, very hard to run stably with two DIMMs installed, and may even be very hard with dual-rank modules. There is a slight performance loss from using 2T rather than 1T, but this will be made up by running the modules at a higher speed. This may not be an option if it is already running at 2T.