RSA KeyPair public key import not working - authentication

Question

I encounter weird problem with RSA KeyPairs in IIS. I have an application which generates signed JWT tokens using private key. I exported public key and I want to use it in another application which consumes these JWT tokens (for JWT Bearer authentication).
Technically there is an javascript client which obtains JWT token from first applications WebAPI backend and use it when authenticates to second WebAPI backend.
This code is used to load public key and setup authentication (uses OWIN startup):
// USE from container
string KEY_CONTAINER_NAME = "MyContainer";
int KEY_SIZE = 2048;
CspParameters cspParams = new CspParameters();
cspParams.Flags |= CspProviderFlags.UseMachineKeyStore;
cspParams.KeyContainerName = KEY_CONTAINER_NAME;
var rsa = new RSACryptoServiceProvider(KEY_SIZE, cspParams);
// Api controllers with an [Authorize] attribute will be validated with JWT
appBuilder.UseJwtBearerAuthentication(
new JwtBearerAuthenticationOptions
{
AuthenticationMode = AuthenticationMode.Active,
AllowedAudiences = new[] { "MyAudience" },
TokenValidationParameters = new TokenValidationParameters
{
IssuerSigningToken = new System.IdentityModel.Tokens.RsaSecurityToken(rsa),
ValidAudience = "MyAudience",
ValidIssuer = "MyIssuer"
}
});
This command I used to import public key to store:
C:\Windows\Microsoft.NET\Framework64\v4.0.30319>.\aspnet_regiis.exe -pi MyContainer C:\PublicKey.xml
This is not working. Public key is loaded and used but never verifies incoming tokens. However, when I load the key right from XML file it works! So I presume the exported XML file is OK. I have no idea why this is happening? Then I tried to export imported public key and compare content of these files. It differs!
This command I used to export imported public key from store (for file content comparement):
C:\Windows\Microsoft.NET\Framework64\v4.0.30319>.\aspnet_regiis.exe -px MyContainer C:\PublicKey_exp.xml
When I load public key from file, not from the store, it works fine:
StreamReader sr = new StreamReader("C:\\PublicKey.xml");
String xml = sr.ReadToEnd();
sr.Close();
RSACryptoServiceProvider rsa = new RSACryptoServiceProvider();
rsa.FromXmlString(xml);