The sill pan should be slightly pitched to the exterior first and foremost.

 

Post a picture of the outside when you get 5 post.
Never seen a "metal" sill pan. Is it aluminum?
There's never suppose to be caulking between the pan and the threshold, only under the pan.
Caulking would act like a dam and hold in the water.
Only ones I use are PVC and there so there's no way water would get in unless the outside was under a flood.
http://jamsill.com/

 

some pics

The pavement slopes. I know the first issue was sealing everything 100% but I was merely hoping I would have zero water penetration, only to find out that I was only trapping water. When I removed the sealant by cutting those 2" air gaps out, the water flowed out, as I expected. I know I need new gutter installed to help remove water dripping off the eave. We also got an unusually large amount of rain when this leaked, which we have not gotten much of in Texas lately.

 

lil more info

I should add, originally I installed the door directly on top of pan because we thought we had the height to clear before hardwoods, but several months later when the flooring arrived realized that was not going to be the case, so I had to uninstall and place the 1x6 treated to raise it another 3/4". Before, I sealed across the bottom with caulk and it handled a few storms with zero water penetration, so when I redid the install a second time, I assumed I could get away with sealing top and bottom of the treated lumber and have zero leakage. The old wood doors installed here had rotted out from time and weather, and we face North-East direction so storms usually move in from the South-West. The pan is aluminum. I know PVC is the 100 yr method but for the $15 and forethought put into doing this pan correctly, I was hoping to minimize water penetration thus extending the life of the sill.

I will remove more sealant and allow the gap so as to let the door breathe. I'll also be installing the gutter and hope this minimizes the water penetration. Just trying to prevent any further warpage on the new hardwoods. They arced a wee bit on a few at the foot of the doorway, so I'm hoping in 4-6 months time they'll settle back into position. Not enough to buckle out of the tongue and grooves, but enough to make you angry after spending two weeks installing them! Always something...

 

Nothing is supposed to hold water. If something does then you have an incorrect pitch or incorrect design.

 

Something looks very wrong from the pics but I'm having a hard time seeing it.Do you have a pic of the pan without the membrane?You didn't put it upside down did you?The sill pan should be open at the top.No way that membrane would lay on it like in the pic unless you wrapped it around the side which looks like what you may have done.It would help to see a pic of the pan without the membrane.The pan should bend down at the front and not be caulked.By caulking you are defeating the purpose of the pan.

 

 

You can to allow for some drainage out in this case. If you caulk the threshold, the water will always get trapped in there.

 

continued

The pan did not run to the end/edge of the "step" otherwise you'd be stepping on and seeing the pan ( about 6" of it would be exposed due to the recess of the door on the slab). Obviously the trade-off on "aesthetics" is that water can find its way in this way, except, it didn't before I raised the door.

The membrane ran up the walls of the homemade pan and I folded around the flanges of the pan. What your seeing is just that but before the membrane was folded over the edges.

I am going to remove the caulking, understanding that it is creating a dam and sealing the pan from breathing.

The pitch is correct.