According to the 328 spec (on the data sheet: http://www.atmel.com/dyn/resources/prod_documents/8271S.pdf), the Flash is rated for 10,000 read/write cycles, and the EEPROM for 100,000 (or 10x more than Flash). I agree one should be careful about excessive access to memory, but my ~2 dozen test runs with one read/write cycle each aren't a concern. It's a good warning to keep in mind, though.
I can post code in about 8 hours, and hopefully I can narrow it down to a very limited set of tests so the code sample isn't too huge. 