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I confirm the result you are getting, but am not sure of there cause and will have to investigate further. Apparently the scriptlevel value that is being set on the upper arrow is being removed. The safe extension does limit the allowed values for scriptevel, but it should allow the value 0, which is what it was set to. I'll have to explore what it happening mere fully.
Please have a look at https://jsbin.com/gapezoravi/1/edit?html,js,console,output, where the upper arrow is smaller than the lower one. This is a strange side-effect of loading ui-safe.
This should solve mhchem/MathJax-mhchem#21.
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