How confident are you that the FPGA design was originally designed and, more importantly, constrained correctly? Is this your customers domain? Are you happy the board is being built with the parts of the same speed grade (the final "2" in the part number) as originally specified?
It's possible that the newer parts you're building with don't perform as well as they used to. They will not be out of spec, just closer to the limit. As a device gets more mature (which I'd suggest your device is) the binning of the devices by the manufacturer get more refined. This allows more parts to pass as higher speed grade parts, higher value, with less margin.
So, if the design was poorly constrained originally you may have had the problem hidden from you. Now with the newer parts your receiving, with tighter margins, the design has revealed it's shortcomings.
If you're confident in your own manufacturing process then I'd suggest this is the question to ask of whoever it may concern.
