In the past when I had issues with not getting all the secrets, I copied the mansion to a new folder and opened it with the level builder and explored the mansion.  Since upgrading to Lion, the older level builders don't work.  Is there a way to do this in the new HD version or am I stuck.  There are some mansions that I have done over a dozen times starting from the beginning and I am still getting the same number of secrets.

Until Vern upgrades the level builder to HD there is no way that I know of to open it in Lion.

You should post about missing secrets in the appropiate mansion discussion board as there MAY be a wrong number of secrets listed in the endgame info.  Then the mansion builder can correct this or at least let us know if there is.

You can use the cheat codes "reveal map" and then "show secrets" (type them in while paused). This will make it so you get no high score for the current play-through, but will help you learn what you missed.

"reveal map" shows the entire map but not any secret rooms

"show secrets" reveals secret rooms too (on the map), and marks them with an aqua tint.