The things to check for are ear mites, ear infections, fleas, any skin conditions, and maybe allergies.
Next up in seriousness is PSOM, an ear problem similar to glue ear in children which can cause scratching and discomfort.
Unfortunately you do also need to consider the possibility of syringomelia as scratchiness in the morning and evening or at night would be one manifestation. Also this needs to be considered when no other explanation for scratching can be found by a vet. All indications at this time are that there is a very high incidence of this condition in the breed and that most cavaliers have the skull malformation that can develop into SM (some researchers believe 50% of the breed as a minimum, probably closer to 85%) .
You can find a whole section on PSOM as well as detailed info on SM at
www.sm.cavaliertalk.com . It is good to be familiar with what to watch out for as a 'just in case' measure, as symptoms are varied and tend to be progressive. Also just be aware that vets will tend to be dismissive of this option, as they are unfamiliar with the high incidence in cavaliers of what otherwise is an extremely rare condition in dogs, according to neurologists.
Most likely there's something minor going on here but the larger concerns should be kept in mind too. Many old time breeders will talk about how cavaliers were always known for having a 'scratching disease' with no apparent cause, which now is thought to have been early, fairly mild incidences of SM.