What is causing /user/*/taxonomy/term/* to redirect to /taxonomy/term/*?
The source of the redirect could be essentially any module you have, and several modules allow for configuration that will cause redirects as well. You will need find the source of the redirect on for your particular situation.
Suggestions:

Deactivate modules in a 50 / 50 manner. This allows you to quickly narrow down which module is providing the redirect, and hopefully that will help you to work it out. Using drush to disable/enable modules will make this much faster.

Install Devel. It has a settings called &quot;Display redirection page&quot;, and implements devel_drupal_goto_alter halting the redirection.
The primary purpose of this is to gather up debug information that would otherwise go lost due to the redirect. In this particular case, I suggest you add a dpm(debug_backtrace()); into the hook so you can trace the call to the source of the redirect.

Everything else failing, fire up a full debugger, and trace the call, ideally with help from the information provided by the debug_backtrace() above.