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Have you tried specifying the feed rate in the z move? Instead of just "G0 Z20", try "G0 Z20 F120" and then "G0 Y200 F3000", for example. Without doing this, it will try to move your z at the last specified feed rate which might be too fast for you z.

tmccafferty wrote:When I enter a g0 or g1 command from the console, it moves fine. The commands don't work though when embedded in the script.

Ah - I misread your original post

flurin wrote:Try with the code M400 (Finish all buffered moves).

I was thinking along similar lines - my end g-code (which moves the head up) doesn't contain a G90 command - perhaps try with this and the Y move commented out.

The M400 was the ticket. This code works very well:

M104 S0 ; turn off estruder heater
M140 S0 ; turn off bed heater
G91 ; set to relative positioning
G1 Z20 F2000 ; move Z axis up 20 mm
M400
G90 ; set to absolute positioning
G28 X0 ; home X axis
G0 Y200 ; move table forward
M84 ; disable motors