This sort of thing is generally a communication problem. Here are some steps you can take to try and find the root cause of this.

Try printing from SD card. If it has the same problem when printing from SD, that indicates an issue with the Brainwave board.Try printing with a different host software on the PC.Export and send us a print log from MatterControl

Also, can you let us know what OS you are using, what build number of MatterControl you have, and your general system specs?