I have had this issue rear its ugly head with Warm and Natural batting while Longarm quilting. It did not affect my tension but what happened is little tiny tufts of batting were being forced through with the needle (and yes this was a brand new needle) through the backing. I later learned these were often referred to as "Pokies". I searched the internet and found a great posting on the APQS forum about it with pictures showing right side and wrong side:
http://forum.apqs.com/index.php?/top...arm+%2Bnatural
I ended up cutting the batting and flipping it over and the pokie problem went away. I do not know if this is an issue with quilting on domestic sewing machines. The needles are much smaller on domestic machines so this would be why the previous posters may say they never checked and never had a problem.
The wrong side/right side up issue would not affect your tension. The only probelm with wrong side up is you can get pokies of batting show up on your back.