Layer 1 won't adhere anymore
The "springs" connected to the stepper motors aren't a problem.  They are special shaft couplers which allow some relief if the motor mounts are not strictly perpendicular to the lead screws.  They are very rotationally stiff and allow just a little bit of misalignment between the shafts.

The first two prints were from the SD card.  You didn't talk about slicing from an STL file, so it is possible that they were pre-sliced for this machine.  Every G-code file has introductory code that initializes some aspects of the operation.  Check the "preamble" code at the front of the files you have sliced.  Are there commands that look different?  Is the Z parameter for the first layer different from the pre-sliced files?  Are there G-codes missing from the files you sliced?

If you are trying to understand what the G-codes do, this resource may be helpful.  Some possible commands could be commands to limit acceleration, jerk, speed, or introduce offsets.  Also check that the temperatures are being set correctly in the G-code you generated.

If you had sliced the files on the SD card, then double check that the parameters were the same.  Try re-slicing the object and comparing the G-code that is generated.