Yesterday, I wanted to see if I could update the plugins on private server enough that I could run 1.11. I use BukkitGUI, and so I went to the plugins tab, and this message comes up:
I believe this is the first time I have checked for updates on plugins after I upgraded to Spigot 1.10.2. I updated not through BukkitGUI, but rather through the BuildTools.jar from spigotmc.org, using the appropriate spigot jar resulting from running BuildTools. I attempted to use the 'Download latest recommended build' button on the SuperStart tab in BukkitGUI, but the jar it downloads never runs. 5 seconds after launching the server, the GUI-downloaded jar causes the server to encounter a fatal error and the server stops. The server and all of my plugins are running normally under the jar from BuildTools, but I can't update any plugins directly from BukkitGUI.
I upgraded to 1.9.4 the same way I upgraded to 1.10.2 (using BuildTools), but while still on 1.9.4, I could update plugins and access the plugin repository.
I really don't want to stop using BukkitGUI. I am aware of how to manually update my plugins, but I'd rather not have to hunt everything down via Google. Additionally, I don't want to have to search Google for new plugins. BukkitGUI just simply makes everything easier.
This is due to the recent changes to BukkitDev. BukkitGUI uses Bukget to grab plugins and update them, which is now being discontinued. It's very likely that the BukkitGUI devs will move over to Spiget, but as always, there are plugins that haven't moved to Spigot.
So no, not your problem. You'll have to do things manually, for now at least.