Make sure you’re using the “GRBL-M3” device profile and not the standard “GRBL” or “GRBL-LPC”. I had a recent project go awry and figured this out because I had selected the wrong one.
It seems there’s some form of bug that when there’s just a single thing to laser in a single scan line, say a | (there’s no laser on/off for a new object), it just… doesn’t. Whereas if there’s multiple items in the same scan line, say a simple U (where the laser turns on for one side, then turns off for the center, then back on for the other side, it comes out fine. I figured this out with a fancy ‘f’ and then did an independent test where all I did was change between the two devices.
Results of my tests are… striking. Sorry for the poor angle, it was a mirror and was being a pain to capture. The lower left one was using “GRBL” as the device, the upper right one was using “GRBL-M3” as the device.
It really shows my bad explanation from above. The center, where it only comes on once for the center of the ‘f’ is completely not there, whereas where it has to turn off and on for the fancy swoops is fine. Why this happens, I have absolutely no clue.
TL:DR2; Make sure to use GRBL-M3 as the device if you’re getting missing lines and skips. 
Also adding this to the first post.