This is how it happened for me and my wife, too: student (me), then changing over to a work visa.
Your brother came in as a dependent on his wife's student visa, not as a visa holder in his own right. Therefore, the same basic terms apply as applied to hers: student time does not count towards settlement, and neither does time as a student's dependent. (If dependent time counted, it would be very easy to scam the system.)
Your brother should count from October 2004 for his ILR because that was the first time he was in the country on a settlement-track -- but, assuming there was no break in residence, he may count from 2000 for citizenship.