Thank you Dave for your question. There is no issue with the program. Nor would I characterize that you are doing anything wrong. But perhaps there's been an update in HEC-22 that you've missed. The latest version of HEC-22, is the 3rd edition, published September 2009. One of the main sections updated was the access hole procedures. On page 7-24 (page 234 of the pdf) there is this paragraph:
In more simple words, inside an access hole, we can accurately determine what the HGL will be. So in HY-12, we assume the HGL to be the same as the EGL (as determining the velocity head is very difficult, even in controlled laboratory conditions).
Does that answer your question and concern?
Thanks,
--Eric