Several fixes have been made to address this. Some will be introduced very soon in a small patch to Wings of Liberty, and some will come with Heart of the Swarm. When Heart of the Swarm launches, there will be a consolidation of code, so players who don't upgrade to the expansion will still get all fixes.
We already have multiple fixes for this issue in the Heart of the Swarm beta, so any reports of the problem having disappeared or still occurring in the beta would be greatly appreciated.
It's a multi-faceted problem. We've seen it caused by GPU drivers, slow hard drives, and even background programs affecting performance. The fixes we've implemented have solved it for a number of specific hardware configurations, but there may be causes that we've not yet found.
Feel free to discuss the subject here, and thank you for your feedback.