We are having exactly the same problem - so at least you are not alone!! 
We are running Version 1.7.1+ (2006101010) and are currently investigating if upgrading Moodle will resolve the problem. We noticed that if you remove any of the resources all the links and icons come back. Not that this helps much… a course with only 8 – 12 resources is no use to us!
We are fortunate enough to have a test bed system and have found that this issue exists on this system as well. The interestingly the system are different though. The test system is running MySQL where as our live system is running MS SQL. The version of Moodle is the same on both though so I’ve checked Moodle Tracker although I cannot find any mention of this or a similar problem.