Something weird is going on, I do the exact same thing and get no packlists, both on Gentoo and on Ubuntu:
Upgrade, See https://github.com/Perl-Toolchain-Gang/ExtUtils-MakeMaker/commit/58ec782413fdfb03f30c0de39131e7eb228f8bc9
How do these parts look in your Makefile?
Pretty much as you'd expect
pure_site_install :: all
$(NOECHO) $(MOD_INSTALL) \
read $(SITEARCHEXP)\auto\$(FULLEXT)\.packlist \
write $(DESTINSTALLSITEARCH)\auto\$(FULLEXT)\.packlist \
$(INST_LIB) $(DESTINSTALLSITELIB) \
$(INST_ARCHLIB) $(DESTINSTALLSITEARCH) \
$(INST_BIN) $(DESTINSTALLSITEBIN) \
$(INST_SCRIPT) $(DESTINSTALLSITESCRIPT) \
$(INST_MAN1DIR) $(DESTINSTALLSITEMAN1DIR) \
$(INST_MAN3DIR) $(DESTINSTALLSITEMAN3DIR)
$(NOECHO) $(WARN_IF_OLD_PACKLIST) \
$(PERL_ARCHLIB)\auto\$(FULLEXT)
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pure_vendor_install :: all
$(NOECHO) $(MOD_INSTALL) \
read $(VENDORARCHEXP)\auto\$(FULLEXT)\.packlist \
write $(DESTINSTALLVENDORARCH)\auto\$(FULLEXT)\.packlist \
$(INST_LIB) $(DESTINSTALLVENDORLIB) \
$(INST_ARCHLIB) $(DESTINSTALLVENDORARCH) \
$(INST_BIN) $(DESTINSTALLVENDORBIN) \
$(INST_SCRIPT) $(DESTINSTALLVENDORSCRIPT) \
$(INST_MAN1DIR) $(DESTINSTALLVENDORMAN1DIR) \
$(INST_MAN3DIR) $(DESTINSTALLVENDORMAN3DIR)
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