A good reference site for how best to create the correct chain length in a jks :-
http://stackoverflow.com/questions/16062072/how-to-add-certificate-chain-to-keystore
Essentially, cat all pem files into one pem file
cat cert.pem chain.pem fullchain.pem >all.pem
Then create a p12 file, this can then be used to import into a keystore, then the chaining count should be correct
openssl pkcs12 -export -in all.pem -inkey privkey.pem -out cert_and_key.p12 -name tomcat -CAfile chain.pem -caname root -password MYPASSWORD
Keytool command to import p12 file
keytool -importkeystore -deststorepass MYPASSWORD -destkeypass MYPASSWORD -destkeystore MyDSKeyStore.jks -srckeystore cert_and_key.p12 -srcstoretype PKCS12 -srcstorepass MYPASSWORD -alias tomcat
keytool -import -trustcacerts -alias root -file chain.pem -keystore MyDSKeyStore.jks -storepass MYPASSWORD