Also note that the profiles are not "flat" or planar. There are out by a very miniscule amount, which can be throwing a tolerance mechanism out of whack.
If you switch to a side plan view and drag one of the edit frames corners towards the other, you will see a "flat" snap appear. Then the file is good as-is (But surely you want to fix the little pieces also)
You may want to review how your profiles became so messed up in Z. Usually, this is a cause of using some type of "make2d" command. This type of output really needs to be looked at before continuing.
Raoul:
<<BurrMan, you are right>>
He is ALWAYS right...
Raoul:
<< I projected the curves to a new XY-planar and used that new projection for extrusion. Now the whole problem is solved>>
I use same trick in cases like this,where there are too many points to check if -REBUILT- not give results
i think in this case -REBUILT-has cutted away not-planar points...