I took a quick look at your 2.5 Bore w/ 1" rod and 2.5 Bore w/ 1.375" rod and I have a couple of comments.
You are expecting the plate with the smaller center hole to have a the higher factor of safety and you are not seeing this. Since you are applying a pressure to the top face the smaller center hole is actually giving you a much larger total force. The “2.5 Bore w/ 1 rod” has an area of 12.26 in^2 and the “2.5 Bore W/1.375” has an area of 14.75 In^2. If you apply a 2500PSI pressure to each face the difference in force is almost 6,000lb. So, the plate with the smaller hole has 6,000lb more load being applied to it.
I am not sure if you are looking at the maximum stress in the model when you are computing your factor of safety or at some point in the model. However, you should be aware by fixing the the cylinders completely and then applying a pressure on the top surface you are artificially increasing the the stress in those areas due to the boundary conditions.
Finally, I would look at running the models with second order elements. this should give you a little bit better results.
Please let us know if you have any more questions.