Hi James
There is no known problem with the SCI in the NE64. I have also used it in several projects with various settings and speeds with no difficulties.
You write that everything is set up correctly but please send a dump of the registers otherwise this can not be confirmed. I can then compare your settings with a known good project using the same values to see whether there is a difference.
Regards
Mark Butcher
www.mjbc.ch / www.uTasker.com