Ok - I found the problem. The way the script was working is by 100 results per page. Apparently this gives you different results if you search by 10 results per page! I didn't know that. So I change the script to 10 results per page. It is a little bit slower but gives more accurate results.
There are just some tools to make you loose a little bit time, because the results aren't accurate. Better work on your site and on google updates you will see your results.
there is always the one available here at DP if you have a google api http://www.digitalpoint.com/tools/keywords/