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I have recently had a similar problem with XOOPS 2.0.16.
I always set the cache folder permissions to 777 but 'adminmenu.php' (which is inside cache) remains set at 644 - which is the normal default for files.
On most sites, updates are no problem, but on one I got the "cannot write to main menu" error. To correct this, I had to set adminmenu.php to 666. (you may want to try that).
I have no idea why this happens. I have re-uploaded clean files so there are no corruptions AFAIK. The only significant difference is that the site which caused the problem is 2 levels down from root, i.e. example.com/subdir1/xoopsdir.
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