I have a rather big custom menu on my site (around 260 links). I don't know when it happened, but I cannot reorder links anymore. After changing weights (with dragging or weight method) and clicking "Save configuration" the page just refreshes with absolutely no confirmation or error message and the changes are not saved. I cannot figure out what causes the problem, maybe some module, but the only one I use for menus is Superfish and Menu Firstchild and I already checked these. Other small menus on site work fine - the changes are saved.
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I found the solution. Submiting weight changes in huge menu like mine sends over 1000 POST vars. Increasing max_input_vars in php.ini (and in suhosin if used) from 1000 to 3000 or more fixes the issue.