I had problem with the follower emotes not showing for me in the menu but after some time i got the info that they don't show if the BTTV or FFZ emote menu are active, atleast the FFZ seem to be the one most hindering this. the one feature that I use FFZ for is that you favorite emotes you have access to, and would you lose access to them and then get them back, they are still flagged as favorite.
This has been very helpful for me since sometime the emote I want to use is not under "Recent" and scrolling down to find the channel that gives the emote and finding it takes too long and chat is way past the subject I wanted to post the emote for. it works as easy as Ctrl+Lmb to flag it.