Two big floods in three weeks entirely possible
I refer to the letter Johor floods: Once in 100 years twice in three weeks?
I agree heartily with pretty everything the writer said except this particular sentence: 'A return period of 1:100 years rainfall means that based on past statistical records, this amount of rainfall has not been encountered in the past 100 years in Johor's history'.
There is a misconception that if a one in 100 years flood happens, then it should be another 99 years until a similar event occurs. This is not so.
Any storm event has a probability of occurring in any given year and in engineering term, it is called Annual Exceedance Probability (AEP). So for a 'one in 100 years flood', it has a 1% chance of happening in one year.
Thus, the probability that two major floods would occur in Johor in three weeks in really very slim. But that doesn't mean that it can't happen although the chances of it occurring are really minuscule.
But it has happened. My guess is that the second wave of floods has nothing to do with the one in 100 years equation. It is just that the drainage system hadn't cleared the first flood waters completely (they are not designed to cope with a rainfall of that magnitude) and the ground was still saturated with water, both causing another major flood to occurr.
Sadly though, this explanation doesn't hide the fact that Malaysia's drainage system are lacking and neglected; the rainforests which form a natural detention basins for flood waters have been recklessly hacked away; the rural areas ruthlessly developed without any long-term plan while corruption proliferates in Malaysia's political system.
Maybe the floods are divine intervention from God himself. Pity they didn't hit the ones that most deserved it.

