My algorithm is PBEWITHSHAAND2-KEYTRIPLEDES-CBC.  I thought that set the mode
to Cipher-Block-Chaining.  I'm pretty sure I tried setting the mode
explicitly to CBC as well, but it made no difference.

I stepped through the Shiro code and could see it doing exactly as you
describe with regards to putting IV on the front of the byte array and
stripping it off for decryption.  However, it didn't seem to do the job. 
It's pretty easy to reproduce with the sample code provided.  (Sorry about
the formatting.)

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