If you make a $90\%$ confidence interval test, the probability to make a type I error is 10%. Then you repeat it. The probability to make a type I error is $10\%$ again. The probability to make a type I error in both of the tests is $10\% \cdot 10\%=1\%$.
The probability to make a type I error in one $99\%$ confidence interval test is $1\%$.
Therefore in both cases the probability to make a type I error is $1\%$.