Honestly it's probably the CPU. AMD tendsto be lower performance per core than intel when encoding. An AMD with more cores would probably handle things a lot better. I hate to plug another site but there is a place where you could roughly compare your current CPU against different ones. Toms hardware used to do CPU charts, and Anandtech hosts this:http://www.anandtech.com/bench/CPU/39
At least it'll give you a rough idea of if more cores might help.
Having only one SSD might bottleneck it to while it's processing, especially if it doesent support trim or garbage collection at idle. What that means is:
SSDs spread the writes out over all the memory cells to prevent wear of any one block of memory too soon. Before new stuff can be written to a used block it has to be erased again, during that erasing the SSD speed can be dog slow (crap) until it's done. If your doin stuff while that happens..stuff slows to a crawl. Most SSDS now "recycle" empty spaces during idle times when the computer is doing nothing. That is what garbage collection is. Trim is the on demand version of garbage collection.
It could be also that the drives just have poor I?O performance and adding another would split the workload between 2 of them.
You may want to look into putting a few more drives in, and doing a raid 0 +1 setup for better I/O performance and reliability. The raid 0 for performance and the 1 means redundancy. You'd need 3 to do that. Putting it in raid 0 also doubles the Apparent capacity as it sees both drives as one and adds the sizes together. So your redundant drive (the "1") has to be as big as the other two together (3 drives) or you need two of them (4 drives)