Hi,
As I understand it, you observe some problem when using the SDI TX. There is no issue when you are running the reference design. However, when you copy some of the design files and build a new project, the TX seems to be not working.
For your information, as I looked at the signaltap screenshot, it seems like there is no activity at the TX side i.e. no PLL lock. I believe either there is no refclk present to the TX PLL or there are some file missing or incorrect path reference after you copy the files.
Since the default reference design is functioning, I think it would be great for you to start customizing from the reference design instead of copying the files just to avoid any missing or incorrect reference.
Please let me know if there is any concern. Thank you.