robzilla - 10:50 am on Sep 28, 2011 (gmt 0)
It's not a stupid question. After a restart, it generally takes a while for the server to fill the buffers to their respective brims. Unused memory is given a task, so that it won't go to waste. The fact that you're seeing memory usage of 97% is a good thing, then, because your server is using memory to its full potential. Any memory not used for applications (such as MySQL, and the OS) is basically assigned a supportive task while it's not required for any vital, primary tasks.
It helps to have a resource monitoring tool such as Munin [munin-monitoring.org] to show you exactly where memory is allocated.