troubles with urls after upgrading

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Hello!
My site has been working on phpwcms for 4 years. But I upgraded cms for the first time only a week ago. I have successfully upgraded it from version phpwcms_1.1-RC4_2004-08-27_A to last available version on today. But after upgrading some errors have been detected. The main problem is related to rewriting urls. When this option is off, urls look like http://webtest/index.php?id=259,2496,0,0,1,0 and work good, but when I turn it on, urls change to http://webtest/259.2496.0.0.1.0.phtml. By clicking on url the catagory containing the article appears, instead of article itself. I have deleted alias of test article (by the way, I couldn't find where it turns off in config and I did it in database) and url became to look like this - http://webtest/aid=2496.phtml, instead of http://webtest/259.2496.0.0.1.0.phtml. Rewriting urls is very needed and it would be great if somebody help me to fix it.
Thanks in advance.