My second attempt was weird. I got, back to back, _A_H_N_T_N _.C. and W_S_I_G_O_ D._. Then Gaborone appeared as both _A_O_O_E and G_B_R_N_, non-consecutively.
It is the de-facto administrative capital of Benin. If you check Jetpunk's World Capitals Quiz as cited above, it treats Porto-Novo / Cotonou the same way it treats La Paz / Sucre and Pretoria / Cape Town / Bloemfontein. Cotonou is not the only capital of Benin, but it is a capital of Benin.
Great quiz! I noticed _A_P_I_A_ had a correct answer percentage of 0% which is a rare sight; I wonder how many others have never been answered correctly.