I've posted my problem on codeplex http://entityframework.codeplex.com/workitem/2087.
There are also some questions posted here but they are not successfully answered.
See
Mapping TPT in EF Code First 4.1 w/ Different Primary Keys
How can I use TPT inheritance models when primary keys have different names?
Is it now possible to have different column names for the primary keys when using TPT? May be with 6.1.0