I'm not sure what might be causing this issue for you. I've not seen it occur on my device, though to be fair, I don't actually use the SMS feature on my own app any longer.
This might see like a very WEIRD recommendation, but you should have a look at an app called "VoIP.ms SMS", which is published by someone who has NOTHING to do with me. However, his app (which deals STRICTLY with SMS from VoIP.ms) is so damned good, that I much prefer using it than I do my own app. He's found a way to support push notifications so it isn't necessary to "poll" for messages.
If I wan't so deeply involved in another project, which is consuming ALL of my time, I would consider re-writing the SMS functions of my app.
So as I noted, it's rather unorthodox for me to recommend using a competitor's app for SMS, but my lack of time and the overall excellence of his app make it this the best advice I can give you.