different results with MEKA vs Scikit-learn!
According to this question 


  LinearSVC is not linear SVM, do not use it if do not have to.


and furthermore


  LinearSVC [is] one of the mistakes of sklearn developers.


In this picture from the question you can observe how it is inaccurate, even compared to SVC with kernel=linear.

Further differences may be explained with differences how SMO and SVC with linear kernel are implemented.

This post compare the two, and the answer is SMO should be the fastest one, otherwise your dataset maybe is not suitable for it.

I would test SVC with linear kernel and see if things change.