I have exactly those problems. iMac Core i7 OSX, Delta with Marlin firmware (also tried latest 1.1 RC7 marling firmware). Also v1.5 had this problem. I hoped that with 1.6 the problem would be fixed. I want to use mattercontrol because of it's features but printing over USB is terrible. Always stopping and giving blobs in the print.
The cause: Mattercontrol is (like other apps) reading the temps of the bed and nozzle during printing. Every time the temps are read the printer stops for 0.5 seconds leaving a blob on my print.
Exporting from Mattercontrol and printing the gcode using pronterface or any other 3d printing app (which also read the temps) results in a perfect print. Somehow the serial communication from Mattercontrol on a Mac is slow (MONO layer).
I dont like Cura but it does the job without blobs.
THIS IS THE ONLY 3D PRINTING APPLICATION WITH THIS PROBLEM!
So please Mattercontrol team fix this problem.