New(?) encryption algorithm

[Hal Feinstein]

This is kind of a silly question.  I recently sat through a 
college level course on telecommunications security that
had a lot of elementary code breaking stuff in it.
Of all the subjects to get hung up on, someone in the class
asked if in counting 2-grams (bigrams) you shoud count every pair
of letters or to tally each pair by sliding a pointer down one
character at a time and taking the character pointed to and the one
to its immediate right as a pair. Well, the class divided.
The heck with traffic analysis and clandestine intercept, this was
really important!  Since then, blackboards have been filled with
math and the college halls filled with people shouting themselves
hoarse over this, the great bigram affair. Really!

Now, I put it to you in networld: which is the "correct" way to
count bigrams?