This is not my particular area of expertise, so I did a PubMed search and found an interesting article that may relate to what you are doing: ‘Characterization of Early Partial Seizure Onset: Frequency, Complexity and Entropy’ Clin. Neurophysiol. Apr 2012; 123(4): 658–669. The essence is that the entropy depends on when in the ictal period you are recording it (onset or established), and the entropy measure you use. Using what these authors determined to be the most reliable entropy measures, entropy tends to be greater later in the ictal period than at seizure onset, when it may actually decrease from the pre-ictal EEG. So your findings seem to be consistent with the literature.
You may not have any problem at all.
