There are no 3GB memory modules. To get 9GB, the user must be using 3x1GB plus 3x2GB for a total of 9GB of memory.
Likely the trio of slots with the 1GB modules is where the problem lies - OR - there is a timing issue between the 2 sets of memory.
What are the makes/models of the memory in use? Also, what motherboard make/model and is anything on this system being overclocked (CPU, GPU, memory)?