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I have created model that take user input from a picklist and then outputs the selected data into an Excel File. When I run the model inside of ModelBuilder it outputs an Excel file that is exactly as it should be. Then, when I save the model and then close ModelBuilder and try to use it in an MXD, the model runs successfully and then give me a path to the output (the very same path that ModelBuilder gives) but when I follow the path there is no spreadsheet.

Has anyone experienced this before?

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Sounds like the output of the Table To Excel tool is set to Intermediate.

Edit your model and right click on the green output bubble and verify it is not set to Intermediate. If it is, then un-tick it as ModelBuilder will delete it at the end of the model run, which would be the expected behaviour as it is set as Intermediate.

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