FC Resource now display a "joint count" and an "apparent joint count" for every design. You can view them on the "Statistics" tab. To understand the difference between the regular joint count and the apparent joint count, you need to understand how joints are made.
If you have three water rods (let's call them A, B, and C), and all three are connected at one point, FC does not connect A to both B and C. Instead, A is connected to B, and B is connected to C, making for two joints. This is the regular joint count. However, if you were to visually count them, you would notice that A, B, and C only joined up at one place, and if you moved this "one joint," all three rods would adjust. This is the apparent joint count, and it would be one in this case.
It's also good to know that the positions of joints are implied. Data is only stored regarding what objects are connected to what objects, but if you overlap two rods (D and E) perfectly, and define D to be jointed to E, there is no way to know which side of the rod the joint is on. However, by default, FC will assume that it is the left most one on rods (before rotation).
A "Neutronium factor" was also added, which is the ratio of the joint count to the apparent joint count.
You can find the apparent rod algorithm in question here, if you want to check it: