I'm think that the first time you re-installed Windows you selected to 'Repair' windows instead of a fresh install, which i suspect you did the second time you re-installed windows. The files are not necessarily gone, but to get them back you will have to find a file recovery program that will allow you to try to retrieve the lost files. The best free one that I have found is 'PC Inspector File Recovery,' which you can google for or go to download.com and search for it. To maximize the possibility of recovery the lost files, don't download anything onto your hard drive until after you have installed and run the file recovery program and tried to recovery the files.
Good luck and I hope you are able to get the files back!