This week's book giveaway is in the OCAJP 8 forum. We're giving away four copies of OCA Java SE 8 Programmer I Study Guide and have Edward Finegan & Robert Liguori on-line! See this thread for details.
I could not reproduce the timing you reported. (Windows 7, java version 1.6.0_31-b05) both keystores loaded very quickly:
java32Programs>%J32%\bin\java TestKeystores Windows-MY
That took 106804384 (0.106 seconds)
java32Programs>%J32%\bin\java TestKeystores Windows-ROOT
That took 218768486 (0.218 seconds)