I think the absence of the par-xxx path(s) in @INC is a key symptom. Does your code modify @INC in any way?
What happens if you build an executable that only prints @INC? Like this (adjusting quote chars as needed for linux):
pp -C -e "print join q{ }, @INC"
If I run it on my windows machine using PAR::Packer 1.047, I get the result below. Note the absence of any of the lib dirs from the perl it was built with.
a.exe
C:\Users\user\AppData\Local\Temp\par-736861776e\temp-21884\inc\lib C:\
+Users\user\AppData\Local\Temp\par-736861776e\temp-21884\inc CODE(0x38
+59d88) CODE(0x385a310)
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