The typical CI formula for Binomial distribution you see in Stats books is using the normal approximation approach. This will not work when p = 0 or p = 1.
The MSA manual is using the Clopper-Pearson interval for binomial distribution. See http://stat.wharton.upenn.edu/~tcai/paper/1sidedCI.pdf
How to compute: (Let's use the example in the manual p.131)
Total inspected (n): 50
# Matched (x): 42
UCI = BETAINV(1-alpha/2, x+1, n-x)
LCI = BETAINV(alpha/2, x, n-x+1)
if x = n, UCI = 1 and use alpha instead of alpha/2 in the LCI formula.
if x = 0, LCI = 0 and use alpha instead of alpha/2 in the UCI formula.
Try it in Excel. You should now have the same result as that found in the manual.