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NewPerfection
Nope, unless you specifically have your slicer set to generate relative movements, you want the G90 there. There's no good reason to do this except for the extruder axis - [reprap.org] There's no real need to use relative extrusion either, though it does make some things easier, such as manually editing the gcode.

The problem is that your start gcode homes the printer again before printing (bold below). AFAIK, this resets the auto leveling. You need to do a G29 after that (underlined below). So, add that line to your Start G-code after the G28.

G21 ; set units to millimeters
M190 S50 ; wait for bed temperature to be reached
M104 S171 ; set temperature
G28 ; home all axes
G29 ; auto level Z
G1 Z5 F5000 ; lift nozzle
M109 S171 ; wait for temperature to be reached
G90 ; use absolute coordinates
G92 E0
M82 ; use absolute distances for extrusion
M106 S255
G1 F1800.000 E-1.00000
G92 E0
G1 Z0.350 F7800.000
G1 X61.893 Y55.213 F7800.000
G1 E1.00000 F1800.000
G1 X62.593 Y54.583 E1.08802 F360.000
G1 X63.283 Y54.083 E1.16766

Edit: Now you won't have to manually home and auto level your printer anymore. It will automatically do it at the start of each print after the heated bed warms up, which is the best time to do it anyways as a warm bed can vary in height slightly from cold depending on what it's made of.

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NewPerfection
You shouldn't need to do anything else. Are you doing G28 and G29 manually before you hit print? If so, does your gcode contain an additional G28 at the beginning? Can you post the first chunk (20 lines or so) of gcode of one of the prints you have done?