Very common when the door is not installed properly, post some pictures and we may be able to help. If a contractor installed this for you get him back there to fix it as this sounds like a very poor install issue.

We did some adjustment. Here are the pictures after the adjustment.

We ajdusted the top and mid hinge a little, very little room to be adjusted but it seems has change the problem a bit. The gap between the door and jamb on the hinge side looks more even when the door is closed. But when the door is open the gap between the door and the jamb above the top hinge is still noticeable bigger than the gap below the top hinge. The first picture is the gap looks like in that area... More or less even to me.

The new problem we are facing after this adjustment is that the door is still hard to close but not because of the door rubbing on the threshhold as it did before. Now it is rubbing on the middle section of the jamb on the lock side. There is no room for the door to go in. We used level to check the lock side jamb. the bottom 3' are plumb, the top 2' are plumb, only the middle section is bulged out. My question is what might be the problem and how should we fix it??

{{!gwi}}
Hinge side jamb is plumb:
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Lower portion of lock side looks plumb:
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The middle section is not plumb, looks like is bulged out towards the door:
{{!gwi}}
Here is the problem area... You can see there is no gap between the door and jamb when door is closed. There is not enough gap for the door to go in smoothly without a very hard push. The middle section of the jamb is blocking the door before we push the door into its jambs
{{!gwi}}

Is it possible your foam pushed the mid-section out? How did you secure the mid-section?

Kirkhall, We used the fiber glass isolation following the mfg recommendation. We tried to fix this problem by drive a long screw into the frame ( where the shims are located) hoping the frame will pull the jamb away from the door a little bit. But this was not effective for this case.

Seems the shims might be a tad too thick.

Thanks for all the help. The shims is loose there but We will try a thinner shims.
The interesting thing is that when we notice the jamb bulge towards the door, we put a long screw into the lower lock hole and we are able to pull the jamb away from the door, but when we put second 3" long screw a bit upper trying to pull upper section jamb away from the the door, it did not work. Maybe we used the wrong screws?

Your initial complaint that the bottom of the door's weatherstripping rubbed too hard against the door's threshold? In your third photo, see the screw in the threshold right next to the bottom of your level? There are several of those screws. They can be turned clockwise or counterclockwise to adjust the height of the threshold stop up or down.

Adjusting those screws would have solved your initial clearance problem.

Hi, Mongcot, thanks for replying. We did adjusted the screws. But the adjustment is not enough. But we did some adjustment on the jamb. the problem of the door rubbing the threshold is less a problem now. We are facing new problem of the jamb on the latch side is bulged out towards the door so the door is very hard to close.
as millworkman pointed out... It due to poor installation... It is so easy to say that. But at which area or how to correct it is what I am looking for.