This is a known issue introduced in Vivado 2015.3 where a XAUI core configured for 20Gbps is not getting synced and aligned.
This issue is caused due to the reference clocks selected in the GUI not being propagated to the GT subcore. Instead the 78.125Mhz clock is taken as the reference clock.
Follow the steps below to work around this issue:
1.Create a separate project with the same settings as your project in a separate directory (this will avoid a file name clash).
2. Click "Add Sources" and "Add Existing IP".
3. Add xaui_0_gt.xci, which will be present in your original project hierarchy where you created the core. It should look like the following:
4. Re customize the added gt .xci and change the reference clock to the one you selected in the original core generation GUI from 78.125Mhz.
5. Generate the core.
6. Replace the gt files present in the original project directory .. xaui_0.srcs\sources_1\ip\xaui_0\ip_0 with the newly generated output files in the new project hierarchy:
7. Open the original project.
8. Select the gt .xci to re customize, and verify that the core shows the correct reference clock you have selected in the core generation time instead of 78.125Mhz.