Hi
There appears to be a few differences but after 300+ years it's not surprising...
Source, IGI (Submitted entries):
B. 1590 Thomas, s. of William Nelson & Mrs Wm. Nelson, Scarning.
About 1609 Thomas Nelson & Elizabeth, Wendling, mar. Note: This entry has Thomas b. 1580 in London.
Source, IGI (Extr. entry):
13 Jan 1591 Thomas Nelson, s. of Edmund, Suffolk, bap. I mention this because of your reference to Edmund.
There are a few trees on Anc. with a lot of unsourced info, it may be worth you looking through those and the IGI entries for something that may attract your attention. It may also be worth mentioning, if your dates are correct, Thomas would be 18 or 19 when he married, not unheard of, but...
Regards
Geoff