Did you replace the battery? You may have a shorted cell, and so you show >12V when operating and all is well, but your alternator is working overtime to charge the battery and pour current into that short (creating heat).

A bad battery can do all sorts of terrible things.

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Current Diesels:
1981 240D (73K)
1982 300CD (169k)
1985 190D (169k)
1991 350SD (116k)
1991 350SD (206k)
1991 300D (228k)
2008 ML320 CDI (199k)
1996 Dodge Ram CTD (442k)
1996 Dodge Ram CTD (267k)

Past Diesels:
1983 300D (228K), 1985 300D (233K), 1993 300D 2.5T (338k), 1993 300SD (291k)