Cascading of S-Matrices using T-parameters messes up S11 and S22?
Figured it out. Clarifying for anyone with the same question.

When I was comparing the S parameters, I was computing the relative error for the individual elements of the S-matrix. The right way to do it is as follows

$$\frac{\begin{bmatrix}S11c&amp;S12c\\S21c&amp;S22c\end{bmatrix}-\begin{bmatrix}S11&amp;S12\\S21&amp;S22\end{bmatrix}}{Norm(\begin{bmatrix}S11&amp;S12\\S21&amp;S22\end{bmatrix})}$$

Where the S-parameters succeeded by a 'c' are the result of the cascaded network and the those without are the result of the composite un-cascaded system.

The elements of the resultant matrix will give the correct relative error. The reason why this happens is because, in a perfectly matched microstrip trace S11 and S22 are negligibly small as a result supposing the composite system has S11=-0.0009 and the cascaded system has S11=0.0003 (linear) the error will be around 133% but one can see that these two are almost equivalent. The above method will hence give a more accurate result.