Your expression should be...
If(IsEqual([Media Sub Type], TV Show), If(Compare(Math([Bookmark] / 1000 / [Duration,0]), >, 0.95), <font color="FFD700">sPadNumber([Season], 2)ePadNumber([Episode], 2) - [Name], sPadNumber([Season], 2)ePadNumber([Episode], 2) - [Name]), [Name])
...which is easier follow written as...
If(IsEqual([Media Sub Type], TV Show),
{true} If(Compare(Math([Bookmark] / 1000 / [Duration,0]), >, 0.95),
{true} <font color="FFD700">sPadNumber([Season], 2)ePadNumber([Episode], 2) - [Name],
{false} sPadNumber([Season], 2)ePadNumber([Episode], 2) - [Name]),
{false} [Name])
You left out the ', [Name])' at the end.
When using expressions, make sure all brackets are closed (i.e., the number of '(' and ')' must be equal), and all mandatory parameters are provided (the function tooltips distinguish mandatory vs. optional parameters).