I'm not sure what is causing it if the file is there and readable (ie check permissions on the file) by the web process.
With the latest mojoPortal release (2.2.9.3) , I did change the default password format for the initial site to Hashed and though hashing doesn't require that RSA key, the CryptoHelper class I'm using to hash the passwords is trying to load the RSA key in its contructor. A couple of people have reported getting this error and it prevents the creation of the initial admin user thereby making it impossible to sign in.
Since the release I have resolved this in svn by just creating a hashing method on mojoMembershipProvider instead of using the one in CryptoHelper class, so I think the latest code bypasses this problem.
If you look in the mp_Users table and there is no admin user there then perhaps this is the cause.
For the 2.2.9.3 release a workaround exists I think by adding this to Web.config/user.config
<add key="InitialSitePasswordFormat" value="0" />
which will specify clear text as the password format for the intial site
then start again with an empty db or clean out all the procs and tables from the existing one, then visit setup/Default.aspx again.
You may be able to change it back to hashed afterwards, but this should get passed the error that prevents the admin user from being created during setup.
Hope it helps,
Joe