There is no "vanilla" ctags, the Ubuntu packages are called `exuberant-ctags` and `universal-ctags` and both install the `ctags` program, but exuberant ctags is actually a debian package, whereas the universal ctags package is maintained by the Ubuntu developers.
As I said Exuberant ctags is unmaintained, the last commit to its SVN appears to have been in 2014, so basically its not what you should be using. So I would strongly recommend you switch.
That doesn't mean the problem will go away of course, but you should try it first.