Are you using an aftermarket EQ at all? If so, try clearing the data in the EQ app.
Android works slightly differently, rather than having EQ's per app/system etc they all tap into a global EQ which controls all volumes, settings globally for all apps that tap into the media output sound channel. The inbuilt EQ option in spotify is essentially just a link to the Equalizer built into the ROM, if (as found in some Samsung & HTC devices) the EQ control is missing from the Android Settings then there is nothing for the Spotify to link to, as such it will remove the option.
If this is the case you need to install an app such as ViPER4Android FX (which is what I use, but does require Root & BusyBox to be installed), or Equalizer and the option will appear in the Spotify app. Clicking on it will take you to the EQ app where you can control the settings.