Hi Bharati

We faced similar issues when using a ASP.NET identity with a custom store. Luckily we could solve it.

This is how my owin startup looks.

public class OwinStartup : UmbracoDefaultOwinStartup
{
    /// <summary>
    /// Configures services to be created in the OWIN context (CreatePerOwinContext)
    /// </summary>
    /// <param name="app"></param>
    protected override void ConfigureServices(IAppBuilder app)
    {         
        base.ConfigureServices(app);            
    }

    /// <summary>Configures middleware to be used (i.e. app.Use...)</summary>
    /// <param name="app"></param>
    protected override void ConfigureMiddleware(IAppBuilder app)
    {
        base.ConfigureMiddleware(app);

        // TODO set correct login path
        app.UseCookieAuthentication(
            new FrontEndCookieAuthenticationOptions
                {
                    LoginPath = new PathString("/nl/login"),
                    //Provider = new CookieAuthenticationProvider
                    //{
                    //    // Enables the application to validate the security stamp when the user logs in.
                    //    // This is a security feature which is used when you change a password or add an external login to your account.  
                    //    OnValidateIdentity = SecurityStampValidator.OnValidateIdentity<OypoUserManager, OypoUser>(
                    //       validateInterval: TimeSpan.FromMinutes(30),
                    //       regenerateIdentity: (manager, user) => user.GenerateUserIdentityAsync(manager))
                    //}
                });
    }
}

This is the code for FrontEndCookieAuthenticationOptions.

internal class FrontEndCookieAuthenticationOptions : CookieAuthenticationOptions
    {
        public FrontEndCookieAuthenticationOptions()
        {
            CookieManager = new FrontEndCookieManager();
            AuthenticationType = DefaultAuthenticationTypes.ApplicationCookie;
        }
    }

And this is the code for the FrontEndCookieManager

 internal class FrontEndCookieManager : ChunkingCookieManager, ICookieManager
    {
        /// <summary>
        /// Explicitly implement this so that we filter the request
        /// </summary>
        /// <param name="context"></param>
        /// <param name="key"></param>
        /// <returns></returns>
        string ICookieManager.GetRequestCookie(IOwinContext context, string key)
        {
            if (UmbracoContext.Current == null || IsClientSideRequest(context.Request.Uri))
            {
                return null;
            }

            var authForBackOffice = ShouldAuthForBackOfficeRequest(context);

            return authForBackOffice
                       // Don't auth request since this is for the back office, don't return a cookie
                ? null
                // Return the default implementation
                : base.GetRequestCookie(context, key);
        }

        private static bool IsClientSideRequest(Uri url)
        {
            var ext = Path.GetExtension(url.LocalPath);
            if (ext.IsNullOrWhiteSpace())
            {
                return false;
            }

            var toInclude = new[] { ".aspx", ".ashx", ".asmx", ".axd", ".svc" };
            return toInclude.Any(ext.InvariantEquals) == false;
        }

        private static bool IsBackOfficeRequest(IOwinRequest request)
        {           
            return (bool)typeof(UriExtensions).CallStaticMethod("IsBackOfficeRequest", request.Uri, HttpRuntime.AppDomainAppVirtualPath);
        }

        private static bool IsInstallerRequest(IOwinRequest request)
        {
            return (bool)typeof(UriExtensions).CallStaticMethod("IsInstallerRequest", request.Uri);
        }

        /// <summary>
        /// Determines if the request should be authenticated for the back office
        /// </summary>
        /// <param name="ctx"></param>
        /// <returns></returns>
        /// <remarks>
        /// We auth the request when:
        /// * it is a back office request
        /// * it is an installer request
        /// * it is a preview request
        /// </remarks>
        private bool ShouldAuthForBackOfficeRequest(IOwinContext ctx)
        {
            var request = ctx.Request;

            if (//check back office
                IsBackOfficeRequest(request)
                //check installer
                || IsInstallerRequest(request))
            {
                return true;
            }
            return false;
        }



    }

This solved our issues. We "borrowed" this code from https://github.com/Shazwazza/UmbracoIdentity

Dave