Porting an environment to Unix involves correcting INI path settings and making sure that all filenames on Unix are lowercase.
If using relative paths and the subdirectory names are identical, then you probably don't have to change any path settings. For example, .\mymrl\myfolder\mydata\myfile.dat will get interpreted as ./mymrl/myfolder/mydata/myfile.dat on Unix.
Try producing PCL output to see if the same overlap issue exists (my guess is it will).
Or you can compare the NAFILE produced on Windows and Unix.
The /NA records will contain the name of the section and the X= and Y= portion will show where the sections are being placed on the page.
My guess is that your Unix NAFILE will have X=0, Y=0 for the sections instead of the coordinates you will see in the Windows NAFILE.
Can you please elaborate on how to fix this.