PCIe comes up but link width is reduced

using Vivado to implment on a Kintex-7 device a PCIe hard core. Got to load and have our linux machine recognize the device. It can see that it is a 4x width device but the LnkSta is 1x. user_link_up is high and when going through debug guide (AR 56616), it only give direction if user_link_up is high and core not seen. I can see the core and my user_link_up is high so any ideas of things to try to debug this.
Should note this is a new board design not on a Dev. board .

I seem to recall debugging a similar issue and finding that you can get a little more information on why the additional lanes did not link up.  In my case it happened quite early in the process and I found that the boards were mis-manufactured with some lanes coupled with 10 nF caps instead of the required 100 nF caps.  These need to be sized correctly for the PCIe lane detection scheme where the transmitters sense the load to determine which lanes are physically connected.

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