If you use CPU core affinity to keep one application from affecting other application on your server, you would be in for a surprise while benchmarking your application with a different core.
Researchers from Virginia Tech have published a research paper indicating that not all the cores on a CPU offer the same performance. Often, interrupts in a CPU are handled by a single core, thus reducing the performance of the applications running on that core.
If you aren't using CPU affinity, you might run into cases where the data that you need is cached with one core (each core has it's own L1 cache) while the software is running on a different cache.
You can get a copy of the research paper here.