Looking at the two examples, the semantic difference seems to tie in to the genders of the words. βαπτισμός and χαρισμός are both masculine nouns, and they seem to describe a process (the act of dipping in water and the act of bestowing a favour, respectively).
The two neuter nouns, βάπτισμα and χάρισμα seem to describe the final result of a process (a baptism is the result of being immersed in water, while a gift/favour is the result of the act of bestowing favours).
I think there's a somewhat similar difference in meaning in μίασμα and μιασμός. The masculine noun stands for a crime - a process - while the neuter noun has at its root meaning a sense of defilement that comes as a result of having committed some crime. It might be stretching it, but it seems this set of nouns keeps the process/result difference between the masculine and neuter forms.
Admittedly, this analysis does not hold up for κλύσμα and κλυσμός. This may be a simple exception, or I may be entirely wrong in my analysis.
I'd welcome any comments/rebuttal on the matter, since my reasoning is entirely speculative.
Hmm, the same semantic difference seems to crop up in πόλισμα and πολισμός. The masculine noun refers to the act of building a city, while the neuter refers to the buildings of a city.