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It seems like you have folliculitis of the scalp which is a superficial bacterial infection of the hair follicles. Treating with the same antibiotics can eventually cause restistance to that.
You did not mention what type of scalp infection your son has been diagnosed with.
Get a culture and sesitivity done each time before you start him on any medications.
Altrnatively you could consult another skin specialist to find out the cause.
Also keep bed linen clean and scalp clean.