i had the same problem. you cant just replace CookComputing.XmlRpcV2.dll. it create conflict with the older version that umbraco uses.
what you need to do is:
1. download the source of PerceptiveMCAPI
2. create new class library project and name it "PerceptiveMCAPI".
3. "drag" the PerceptiveMCAPI folders that you downloaded earlier. (i used only the PerceptiveMCAPI folder).
(by the way: i had to delete the AssembliInfo.cs file from my project and use the one that come with PerceptiveMCAPI in order that it to work)
4. copy the CookComputing.XmlRpcV2.dll from the umbraco bin into the bin of PerceptiveMCAPI, and add it as reference.
5. recompile everything. now you have new version of PerceptiveMCAPI, that uses the same CookComputing.XmlRpcV2.dll version that your umbraco version is using.
6. add only the PerceptiveMCAPI.dll as reference to your umbraco project (user control or whatever) and use it as you like!