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I'm also having the same issue.
I use chef to manage my jenkins config files (jobs, plugins, etc), so whenever one of these files is edited by Unix tools such as VI, a newline is appended to the end of file, causing the file to be reloaded everytime chef is applied (since it's different from the jenkins parsed file, without newline).
I don't remember having this problem with verison 1.563, but now that upgraded to 1.590 started happening, so probably it was introduced recently.