The TeX filter relies on several binaries that are optional packages on many Linux distributions, latex, dvips, convert. These were probably not installed in the new system or put in a different place than on the previous system. If these are not all present, the filter default to using a different method that produces poor output. You need to make sure that texlive and ImageMajick packages are installed and the paths are set correctly in the TeX notation filter settings page.
Mathematics tools
Hugh equation
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