Actel has violated a rule in design. They over-engineered Libero IDE. Libero attempts to automate constraints. Here-in lies one class of problems.
Libero determines all of your clock constraints from the MSS setup. Those constraints are then hard wired into the Designer project. There is no pdc file to edit for the clock constraints. These constraints can't be edited using Designer's constraint editor because the automatic constraints are read-only.
Why is this bad?
Libero has a bug where it sets the constraint incorrectly if you set the divider of GLx to a non power of 2. Divide GLA by 3 and the constraint is set as if it was divided by 2.
In general, over-engineering complicates both users' and developers' lives. I am referring to customers as the users and the Actel employed programmers as the developers. Over engineering creates for confusion as nothing is intuitive anymore. It also opens the door to many more bugs.
Xilinx is an example of a high quality company that doesn't over-engineer (from what I recall). Their tools are not great, but they leave all of the configuration in your hands. Even if they tried to automate something, they still let you override whatever it is.
Another frustrating problem is how Libero splits constraints into 2 places. I recently configured an MSS I/O to route to the FPGA. I did this because I needed Schmitt Triggers. What is overly confusing is how the default constraints file located under component/work/
The solution? Under the MSS configurator there is a middle tab for I/O Attributes. Use that tab. That's not all folks! Now you must add a new pdc file to the Designer project. I imagine that if you hit the Designer button in Libero it will add the new pdc file to the Designer project, but as I rarely hit that button, b/c Designer is already open, I can't say whether this is true. But not only must you add this file, you must also remove any reference to the incorrectly placed constraints from the original pdc file. The MSS I/Os must only appear under the MSS pdc file.
Folks at Actel seem to have forgotten what simple and intuitive means. They should refresh their memory.