I moved this question to the firmware section as it is not specific to Cura or plugins.
Your problem sounds a bit like a firmware bug we had over a year ago which resulted in the last 250 bytes of a print being ignored. I don't remember exactly, but this was about Cura version 3.2 in combination with firmware from that revision or older.
Cura 3.3? or newer are shipped with a firmware that fixes this problem.
What version of Cura are you using?
Which firmware version are you using?
Have you tried updating the firmware?
btw I use Ultimaker2 as gcode flavour and nothing customized
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