We'd need to know what was there and what errors/warnings were received; we don't have your hardware so no way to have any idea what's happening...
However, you have a lot of extraneous overhead in your logData function -- similarly as to passing the file handle in fid, create the axes objects for the plots first and then plot into the axes handles. But, even more than that, don't call the high-level plot() routine at all; depending on the effect you're after use animatedline or only update the X/YData arrays after having drawn the initial plot instead of drawing the whole graph again.
There are examples and suggested ways to improve animation in the documentation for graphics section you can study.
But, at some point with realtime acquisition you will simply run out of compute power -- I do not have and so haven't ever experimented with the parallel toolbox; ergo I don't know how effective of use one could make of it for this purpose but that might be one direction to explore eventually. But, first work on the overhead in the existing code.
