I am liked by the NCR. People are always saying I am a good citizen etc,, helping everyone I come across. I went into the far part of the strip where vault 21 gift shop and the NCR headquarters for the strip are, and a NCR MP Trooper comes up to me and tells me they don't like my mojave scum kind etc.. and I either have the choice of giving him 200 caps or fighting what did I do wrong? Why are they doing this?

You might be wearing a disguise. If not, that's probably a bug.

Yeah no disguise here I guess I will have to pay him so they don't get mad at me

Why is this in cheats hints and spoilers? Its a game issue not any of the above mentioned. Trying to find out what is wrong with my game.....

Yea, another thing dont steal anything infront of the NCR either. I stole one cap, just one cap in the air port and one NCR guard saw she came up and next thing I know she didnt take the 1 cap from me but took all my weapons, all my aids, all my clothes, ect. She took everything and I didnt like that so I had to resort to blowing her head off.

I kind of think that is excessive so I think this is a bug where you steal a cap get caught and then those NCR bastards strip you of everything over a lousy cap laying next to a slot machine.

This happened to me too. At first I blew by the MP in the street and talked to the ambassador. I gave him good news and gained NCR fame. When I was done the MPs came after me in the hallway as enemies spouting off about how I should have paid and I now I had to die. (Reminded me of Oblivion guards ("You should have paid the fine!") The fight carried into the street and when I tried to flee the robots on the strip killed me.
Reloaded a save and enter the area and talked to an MP first. He shook me down for 200 caps and the rest of the meeting with the ambassador went smoothly.

My thoughts on why this happened.
A. I had just told Yes Man that I helped the Omertas. They are planning something bad for the strip and the NCR might not like it.
B. I also told Yes Man that The Boomers would help at Hover Dam. (also what I was on the way to see the Ambassador about.
C. I had entered a restricted area out in the wasteland (some electrical station) and the rangers there went nuts and I had to kill them all. It is possible word got back.
D. The dealings with The King are complex. He and the NCR are not getting along because of Pacer's actions. I was involved in a battle over the water rights and that might have triggered this.

I am liked by the NCR so I don't know why the MPs hate me.

Those NCR bastards are a picky bunch. While at Helios one I desided to salvage the broken solar reflectors while I was there next thing I know the whole base goes ape[censored] over me saluaging broken reflectors. They also went ape[censored] over me killing their guard dogs in the east terminal even though I was helping to activate the power plant. But yet on the first play through I had on a NCR officers uniform and got in killed the dogs and got out with no problem.

This. NCR doesn't react well to you murdering their troops, nor does it react well to entering the El Dorado substation.