Having the same problem and cannot find a fix. max_vars (suhosin) and all other var limits set to 9999999 from 200, confirmed in phpinfo and still no joy. No matter what I do I cannot get any more than 15 menu items, yet I can post an array of 1000 arrays with 1000 vars in each without problems.
No errors anywhere, of any kind thrown – looking at the print_r of post shows 15 menu items only to the truncation is happening on post.
Weird twist – if you post more than 15 menu items, all menu items after 15 are dropped and the last visible (#15) menu item is switched to custom.
This is the one item preventing a site going live… Suggestions?