edit-user-talk (i.e. talk page messages on a non-Flow user talk page, as indicated by that orange bar) has also been moved to Messages. That means seeing both icons will not be rare, even without Flow, so I think it's worth always having the icon to reinforce which you're seeing.
Is there a way to check which commit of Echo translatewiki.net is using? This was merged a couple days after the split, so that might explain why you're not seeing it.
twn:/srv/mediawiki/workdir/extensions/Echo (master)$ git show HEAD commit 9a2262d6949474351d5de2a6a81e9cfff6de0a3c Merge: 582017e aae891d Author: jenkins-bot <firstname.lastname@example.org> Date: Tue Sep 8 21:13:53 2015 +0000 Merge "Use #pt-notifications-alert to get Special:Notifications link"
Our updates are regular in irregularity, but usually only few days apart.