Navigation-menu problem

Hi guys … I seriously need help i am going crazy :

I have wordpress site , and having big problem with navigation menu .
My navigation menu have 6-7 root nodes, but some root nodes have very big tree beneath . Recently, i set-up .htacces and and maxinputvars to 5000 so , even my menu is quite big i didnt have problems. But today very strange situation happened: When i opened my website in browser , navigation menu was completely crashed : all submenu items from biggest node suddenly became main nodes …reason is ununderstandable : i didnt change anything today,loaded site in the morning,everything was good, but in the afternoon i saw a catastrophe . Important thing : when i saw crashed menu i got my sql database backup file and import into phpmyadmin… Opened site -all looks good. But when i click any single menu item in site , menu again crashes with same problem ? Can somebody help ?