while sighting it for 50m, i had to raise the front sight post WAY out of its well.  the threads are still connected, but the little platter with the notches is as far out of the well as the platter is thick (dont know the technical name for the notched area of the front sight post).

is this normal while sighting in a 3rd party BUIS?  the iron sight that was in the carry handle was of course dead on with the front sight seated as from the factory.  anyone else seen this type of thing?

It seems unusual. You can always buy a taller front site post for a more normal "look". I have troy BUIS on three of my middies and its not a problem with a F marked  front sight.

A taller front sight pin will fix you up.

Check out this thread.
http://www.ar15.com/forums/topic.html?b=3&f=66&t=344624

I think you got the wrong rear sight...

From Troy... Note: Sight is designed to work on same plane rail systems only. Will not work with a railed gasblock that is higher or lower than the receiver.

I assume you have a A2 front sight, correct?

What front sight are you using?  If you have an A2 and it is not "F" marked then yes, you will need a taller front sight post or simply replace your front sight base with an "F" marked FSB.

The statement from Troy refers to their front BUIS.  The Troy front will only work on a railed handguard.

I use a troy buis and have non f marked fsb. No taller post needed for me. Depends on your rifle.