Sounds like the buffer is running empty. Try disabling filament preview which takes more and more time with increasing complexity. Alternatively use repetier-server as printing engine and connect through host for usage like you are used to. Server has no change on different gcode sizes, so speed does not depend on this. Last speed increasement would be to switch to repetier-firmware with binary protocol allowing faster transfers through smaller command sizes, but normally should work also without.
This is a problem especially with fine grained small segments as you need to send more commands in the same time to keep up the speed. Speaking of speed - slower printing is also a solution, but who want's to do that:-)