I'm interested as to why you are using Rijndael over a different cypher. Is it because it is the official AES algorithm?

There is no doubt that the algorithm is strong, however, if you have chosen it soley on its AES merit, then perhaps this may not be the algorithm for you.

Why do i say this? because there are other algorithms out there that may be easier for you to implement in perl ,not to mention the difference classes of encryption algorithms (asymmetric, symmetric), performance difference between different algorithms, or the type of data you want to encrypt.

This node describes the difference between cypher block chaining and non cypherblock chaining and how to implement both in perl (via cpan modules). Here is a link to a bunch of cyptanalysis of different algorithms.

In short a CBC will encrypt/decrypt a message of arbitrary length, which is what I'm guessing you'd like to do. Just becuase the algorithm isnt marketed as "strong" (ala AES) doesnt make it weak. Consider a runner up in the AES finals.

Remember, dont always go for the marketing.