Why does Drupal not register Menus Nor Links?
It would be interesting to see if your problems could be related to the "memory limit", which might not be high enough (anymore), especially since in the OP it says "I have many modules enabled".

I'm assuming that this is NOT a multi site. So therefor consider editing your /sites/default/settings.php, and change the line to set the memory limit. If it is a multi site, then edit the settings.php file related to the site where you are experiencing the problem.

That line in settings.php should look similar to this:

ini_set('memory_limit', '100M');


The '100M' in it might be some other number. Whatever the number is, try to increase it with like 50%, or maybe even double it to see what happens after you do so (of course do not forget to save the file after increasing that number).

Curious to hear if that helps somehow ...

Here are a few other thoughts that might ring a bell in the right direction (if you haven't tried them yet):


temporary turn of all caching, to see what the impact is of doing so. Of course that cannot be the real solution in most cases, but at least it might give some indication like "it seems to be caching related".
what about compression of JavaScripts and/or CSS? If you have turned them on, what happens if you (temporary) disable them?