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Black isn't black. It can be IR transparent dye (as in IR sensor package) or some IR absorbing material. Another possible problem is crosstalk due to surface reflection. Did you try with increased TX to RX separation?
By the succinct description "the IR doesn't work", do you mean that it detects when it should not, or simply does not detect at all? As a rule, since you are using the same optical barrier for both, it would be ideal to put them as close as possible to the surface and add a housing around both emitters and receivers in order to avoid the return of light, as FvM mentioned by internal instead of by external reflection.
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