If you need to export an FLV file, then use the previous version of the application.
See this for an explanation for the change regarding FLV and F4V and for the recommended workflow:
removal of FLV and F4V export features from Adobe Media Encoder, After Effects, and Premiere Pro
See this for an explanation for the change regarding H.264, MPEG-2, and WMV and for the recommend workflow:
using Adobe Media Encoder to create H.264, MPEG-2, and WMV videos from After Effects