From the sequence of output below it seems clear that ScriptCraft is echoing the warning below. There might be a Read operation that isn't coded properly for end of file or the reader going out of scope. Or there could be a config issue, but I don't see any config issues and have tried to modify files with no success in eliminating this message, so I think it's a code issue.

[Server] INFO Please note that the working directory for scriptcraft v3.2.0-2016-03-19 is /scriptcraft
[Server] WARN Please put plugins in the /scriptcraft/plugins directory
[Server] WARN Legacy ScriptCraft directory /plugins/scriptcraft was found. This directory is no longer used.
[Server] WARN cow-clicker minigame is not yet supported in CanaryMod or Craftbukkit
[Server] WARN Could not connect to dev.bukkit.org, please try again later.
[Server] WARN :1:1: Premature end of file.
[Server] INFO No updates found!
[Server] WARN The updater could not find any files for the project id 31279
[Server] INFO Enabling scriptcraft v3.2.0-2016-03-19

I can't reproduce this issue.

As discussed in #309, I'm thinking an update is being requested, nothing is coming back, then a read is done on an empty file. With data expected but not present, the updater might be generating this warning.

What's confusing is that you don't see the same error. Let's see where #309 goes and closing that issue might also close this one.