Brent help to solve this problem, but we are not exactly sure why.
After he had me test various functions in the hotkeys program, the Bibles would index properly and subsequently showed up in the Bible Select window. The time it took to run an indexing of a particular version increased by 2 or 3 times to between 9 and 19 seconds each. So this to me meant that something was not being executed in the original attempts to index the versions when it failed.
The only thing that I can guess (and it is just a guess) is that some variable was not initialized properly until we used the hotkeys.
The end result is that everything works now.
Thanks for your help, Brent.