SGD vs SGD in mini batches
My understanding is that mini-batches are not really for speeding up the calculations... but to actually allow large datasets to be calculated.

If you have 1,000,000 examples, it would be tricky for a computer to compute forward and backward passes, but passing batches of 5,000 elements would be more feasible.

For your case, I recommend you two things


Try different batch sizes.
Make sure you shuffle your batches!!! that will certainly help you a bit.