I just lost half a day to this issue, so I thought I would share this find so others can avoid this pitfall.
We have a game that loads levels, these levels are individual asset bundles that are loaded at runtime. We tested a level and then made some changes. The changes didn't show up? OK, bundle the level again and upload. No change. Delete the level, upload again. No change. Delete the level. THE LEVEL STILL LOADS?!
Turns out, even in the editor, Unity uses the web cache. You can see your project using the web cache here: http://webplayer.unity3d.com/setup/ - it looks to me even if you check "Disable all caching", it still caches.
So if you are using asset bundles and you make a change but your asset does not seem to update, delete the web player cache.