The biggest issues are with the first two boots after installing a new ROM. It takes awhile for each process, app, or service to be called upon for the first time. The first time, each of these has to do extra processing and communication with the kernel/OS. Much of this initialization is then cached, so the next time that app/process/service is run, it takes less time to start up, and less processing cycles to perform it's functions. Once most of these things are cached, the entire system uses the processor less, so everything begins to run smoother/faster.
Kinda like a stove. The first time you use it, you have to hook it up, figure out what does what, make sure everything is safe, and then you can use it. The next time, all you do is use it, much faster.
