G'day Mjolinor,
Slicer several versions i've tried seem to have similar effects, thou I did think that it was the slic3r program which was making bad G-code, i am not 100% convinced now that it is after trying the latest version, and the experimental version.
I was using slic3r version 1.0.0RC2, then switched to version 1.1.7.
The same sort of things happened with the latest version i also tried version 1.2.4b experimental thou it didn't provide my requirement to import multi part stl files.
I am using a SD card, thou I switched to this as just after I built my machine the seemed to be bugs when printing through the USB.
I tried disconnecting my cooling fans, to try if there was an issue with noise from them, no luck. One print I am using as a test to see if the problem is fixed plays random moves on the first layer, and its not a complicated print.
I am using a Ramps 1.4 board with a Arduino Mega 2560.
Cheers