If mixing JIS crown races and ISO cups is an issue, I guess I'll find out someday, because I have two bikes that have that combination and have been that way for a long time. That happened by way of experiences pretty much the opposite of bigbossman's - I ordered new ISO headsets only find that their crown races wouldn't fit on the forks I wanted use. So, I just polished up the old JIS crown races and installed the rest of the ISO headsets. No apparent issues so far.

Of course, this occurred before I discovered that JensonUSA has an entire page of just crown races, and that I had overlooked the option box for selecting either 26.4 or 27.0 when ordering the headsets.