Do you notice if your engine revs dip when this happens? This happened in my Mazda 6 at lower speed (e.g. coming to a stop light). There was a bad coil pack that caused a misfire. However, electric issues, fuel pumps, transmission slips and more can cause this behavior.
I bought one of the cheap ODB scanners (Bluedriver) to use on my 2006 Mazda 6. While this does not replace a higher end
scan tool, you can at least see for yourself the various codes being sent.
Also, you said you had your car in the shop. What this a dealer, Hyundai shop, major chain?
Anytime you have a tough problem in a car, taking to a dealer may be better. I don't think dealers are any better than others at routine repairs, but with difficult problems, their experience can help.