I run an i3, and used to have this same problem. Your first layer is transparent because you are printing too close to the bed. Your nozzle is dragging. Reset the z-axis height at the center of the bed. Get a set of feeler gauges. Paper… Ok.
Now grab your bed, if your skipping in the y direction (front to back) tighten belt, ensure glass is very affixed to bed. Four metal clips will not hold the bed as you start to really print with the i3
Grab you head, if skipping on X and only a touch of Y your hotend, you’ll notice, has some movement. Tighten this movement, lots of solutions. Then make sure this belt is tight.
Another thing : how is you fan configuration? I’ve one pointing on the bed and one fix to the hot end body (I’m printing pla) connect to the heated bed power. The result is not bad but the hotend temperature sometimes go below the 180 degree e.g. this configuration is cooling too much. How can I solve this? How can I control the hot end fan speed ?
My brother had a similar problem: it was the belt. Sometimes on fast movements/accelerations, belt slipped because it was not well tight. So it shifted all the next layers.
Make sure your motors have enough power. When I dial in the power to the motors on the stepper drivers, I make sure it is strong enough by pushing on the axis in quesion and moving it manually in the opposite direction in pronterface. If you can move it slightly it isn’t powerful enough. turn off your machine and advance the pot on the driver a hair more then try again. this works for me and I don’t have that problem anymore.
Not sure what controller board you are using, but I had a similar issue with my i3 with a Rumba controller. I tried most of these suggestions and then saw something on the reprap forums suggesting that perhaps the Rumba was the issue. I changed the channel that the Y-axis runs on and now it works perfectly. It wasn’t the driver itself, but something on the Rumba board itself. The thing that tipped me off is that at one point I actually saw it do the skip and it actually added steps rather than skipped them.