According to Nikon's compatibility chart E-Type lens are not compatible with the D90. This is probably why you can't change the aperture.
"Nikon D2-series, D1-series, D200, D100, D90, D80, D70-series, D60, D50, D40-series, D3000, and film SLR cameras will not communicate aperture information electronically and cannot be used."
"Nikon D2-series, D1-series, D200, D100, D90, D80, D70-series, D60, D50, D40-series, D3000, and film SLR cameras will not communicate aperture information electronically and cannot be used."
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