Any time I have lost the value of the drop-down it is because I messed up and repopulated the drop down before handling the value change. For me, it has been drop-downs that I need to do something special with like add item attributes for Javascript, etc. This is data that needs to be added on every page load (aka data that is not persisted in the drop down like the names and values of each item). In these cases I have done this work on load, then I try to retrieve the value later in the page lifecycle and DOH!
Here is the page lifecycle:
http://msdn.microsoft.com/en-us/library/ms178472.aspx
Dollars to donuts that is what is happening. You are probably just reloading the items before you get to handling whatever postback event you are using to grab the value. If you are doing this and cannot get around this work flow, just save the selected index at the beginning of the logic that populates the drop-down, then set the selected index of the drop down with that value when done.