I don't know what is wrong with your code, but I have code that reads stuff from a key store. I read the file into a KeyStore instance and then access the key or entry as appropriate. Here are some of the relevant calls:
char[] password;
String alias;
java.security.KeyStore keyStore = KeyStore.getInstance("PKCS12", "BC");
keyStore.load(inputStream, password);
java.security.PrivateKey privateKey = (PrivateKey) keyStore.getKey(alias, password);
java.security.keystore.PrivateKeyEntry privateKeyEntry = (PrivateKeyEntry) keyStore.getEntry(alias, new KeyStore.PasswordProtection(password));
To find the alias of the entry you are interested in, I suggest using keytool (comes with JDK):
keytool -list -v -keystore keystore.pkcs12 -storetype pkcs12
You will be prompted for the keystore password and then get information like this:
Keystore type: PKCS12
Keystore provider: SunJSSE
Your keystore contains 1 entry
Alias name: thealias
Creation date: Aug 30, 2013
Entry type: PrivateKeyEntry
Certificate chain length: 2
[... lots of info about the certificates deleted ...]