participating in language is like playing a 2000 year old game of telephone

this is because enkephalin is derived directly from greek (εγκέφαλος) whereas encephalitis is derived from the (new) latinized "encephalon" (which is derived from the greek)

however even if greek weren't involved here you would still have the same problem because "c" in classical latin is generally pronounced as /k/ whereas in ecclesiastical (church) latin it is usually pronounced /t͡ʃ/. a good example of this most people know about is the 2 pronunciations of "Caesar". another medical example is the class of cephalosporin antibiotics, some people pronounce it with /s/ and some with /k/

and of course just to make it worse the latin and greek terms for something are often completely different and are both used for different derived words. like ren/nephros for the kidney (whence both "renal" and "nephritis"), pulmo/pneumonas (whence "pulmonary" and "pneumonectomy"), diaphragma/phren, etc. (actually both of these are greek terms for the same thing lol)