I installed ReSharper 3.0 RC1 over 2.5.2 and when it prompted me whether I want to keep existing shortcut keys or reset them to the new keyboard scheme. I chose to reset to the new scheme. After that I changed some of them (eg. GoToType, GoToFile, FindUsages) to use the old shortcut keys again. I then installed RC2, Gold and now 3.0.1 and each installation has reset all my shortcut keys again - without any prompt.
This is quite annoying and it's a blocker for us upgrading as I don't want all developers in the team to waste their time re-creating shortcut keys every time they install a new version. It didn't happen in 2.5.x.