Doesn't print on top of first layer

After building and calibrating my printer I started printing a few 10mm test cubes.
For now I'm happy with the results, it's not a perfect cube but it is getting close.

However, when I print larger objects the second layer is not printed on top of the first layer!
For some reason the second layer is closer to X Home than the first layer. This happens with every larger print I tried, note that 10mm cude doesn't have this problem.

I connect the printer to my laptop via usb, use Slic3r to generate G-code and user pronterface to load the file and start the print.
A fan keeps the stepsticks cool.

I have no idea what the source of the problem is.
Hope you guys can help me out.

Printer info:
Prusa i3
Megatronics v3 with Marlin firmware
Slic3r v1.1.7
Printrun 2014.08.01

Laptop:
Ubuntu 14.04 (I keep everything updated)

You might be having issues with your motors skipping steps and causing the second layer to be offset from the first. A picture of the issue would help confirm/deny this, but from what you're describing that sounds like the issue.

From what I know, there's a few ways to fix this and you might need to do a combination:

1 - tune your stepper driver VRef up so the motors get more current without getting either the driver or motor too hot.
2 - tune down the maximum velocity and acceleration for the X and Y axis in Marlin. The default values are silly high
3 - make sure your belts and pulleys aren't slipping
4 - turn on motor holding in Marlin, if it's not on a motor that isn't being used but was last in a mid-step might reset to a full step resulting in inaccuracy

Also make sure your first layer isn't too squashed. That can create ridges that really grab the nozzle on the second layer and can cause skipped steps.

Thanks for the info.

I should have been more clear in the first post.
The second layer is not of by a little bit, the printer really goes a few centimeters towards x home for the second layer.

I'm starting to think my hardware is broken because I'm having another weird problem.
[forums.reprap.org]

Here are two pictures of a failed print.

The bottom and first layer were printed correctly.
The second layer is off by about 7mm.

Hello,

Have you calibrated your stepper motors so the software knows to step the motor so many steps per mm?
There is good guide here Triffid Hunter's Calibration Guide
getting the steps value in the firmware correct for each of your axis (x,y,z and e).

As looking at the photos and you stating it's off by 7mm, your steps_per_mm values within the firmware could be off on 1 or more axis.
It also looks like it's over over extruding the E axis also.

This page gives open scad details of a good XY Calibration object XY Calibration Object
It's a 100mm x 100mm square and quick to print, mark up the axis before removing from the build plate, then measure; you might find that one side is more or less than 100mm. Using the forumla mentioned in above guide you should be able to adjust the value, then re-print the process until you get both axis measuring 100mm within 0.5mm or less.

Hope this helps you

Thanks to all for the advice and tips!

I tuned the stepper driver for the Y axis, the voltage was set too high.
And I lowered the default max acceleration from 9000 to 6000 for the X and Y axis.

The print is now near perfect.