If it is not including same rows everytime, it might be bad data in source.

Since you have to manipulate data, what you can do ( which I did too) TRANSFORM your XML files into smaller xml files and during transformation manipulate your data. Than...

For quick learning, try this article:

http://www.sqlservercentral.com/columnists/lplatt/20010422115709_1.asp

I had a similar kind of situation, therefore, thought to share, may be this gives you some idea:

I had a very large XML file received from one of my company's...