Thanks for your reply and comments. It's interesting how designs change over time. Even on this thread, some have suggested that the cups need to be seated all the way. Phil Wood defends their design and says its perfectly acceptable to have exposed threads. I learned a lot. I knew there were different thread types (as in pitch/size) but did not know that the French and English wisely changed the DIRECTION. Now I know why.
I do not have pictures of how the bottom bracket was installed the first time but it looks identical to me - about 2-3 mm of exposed threads on the drive side. The NDS cup is flush with the rim of the bottom shell.