I had a similar problem when i first started using lightroom. It said that the files already existed in the location your trying to import. I can't remember exactly how I resolved this, but I think what I did was blow away the folder in Question and then re-import the whole folder with the ignore suspected duplicates box unchecked. Then you should have all your pics in the same folder. Even if there name is the same.
This was only an issue for the old folders I had on my PC with old pics that I was trying to import an organize.
All the new stuff I import directly from my Camera card to Lightroom and convert to .dng files. Then I edit them in Photoshop right from Lightroom, so Lightroom doesn't have the duplication conflict.
I hope that helps you out
Jay