Can you attach your two versions of the .vapi? On Ubuntu 17.10 they are almost identical and would compile against either one.
Attached.Now, here is a diff from the bad PackageKitGlib-1.0.gir in my 3.25.90 build to Rico's good gir: https://paste.gnome.org/pmdfo1n2i/laa4ak/raw. Lots of differences there, all related to enums. glib-mkenums has seen a lot of churn recently, so glib is what I'll be looking at next.
Michael P.S. Nice meeting you at GUADEC, Robert!
Attachment:
packagekit-glib2.vapi
Description: Text Data
Attachment:
packagekit-glib2.vapi
Description: Text Data