You could post a sample Word file and we can take a look. Also specify what version and language edition of Word you are using.
If you are using Word 2007 or higher, you are probably using the built-in Microsoft Equation Editor to format equations. If you open a Word file and place the cursor inside an equation, then an "Equation Tools" tab will appear in the top window title bar. There is also a possibility that you are using MathType from Design Science instead, and I think "MathType" will appear somewhere in this case.
Once you save the file in plain text format, all formatting, including any maths, will always disappear, so you will never be able to import into Moodle from this format and retain equations.