ISR driven UART is missing characters (even at 9600bps... same prob at 230400)

Glad it could help you. And just like dsl said.... My problem was all in how the ISR was handled, the code was fine--I had effectively shot myself in the foot with the NIOSII configuraiton (lots of cache/etc..) That's what makes problems like I had so complicated to fix... there was nothing wrong with the 'C'... it was in how I had configured the NIOSII and the UART... enlarging the buffer and leaving the CPU alone, I was able to run all the way up to 250Kbps (which is the limit of the DE2-115 level converter--e.g. as fast as my hardware could support.. the FPGA/NIOSII/UART could have gone faster.)