the new pcilib have a PCI domain parameter in additional to the BUS:DEV:FN. I think you are using old pcilib, just removed the 0x00 parameter.
When you say "new" pcilib you are talking the _alpha_ pcilib 2.1.99. The latest stable version does not have this domain parameter.
The 2.1.99 alpha is not backwards compatible with the stable so you can't just update your libs since it causes lots of other things to break.
What I ended up doing was creating a private pcilib lib in the vgabios dir and have testbios use that rather than the system library.
What was the a reason you had to move to the alpha version for the userspace program in V2? Seems like a lot of trouble for not much real gain.
BTW, the int1a implementation in testbios (both V1 and V2) is not necessary correct. Yout should take a look at src/device/emulator/pcbios/pcibios.c in V2 tree.
What parts exactly did you fix? I took a brief look. The lack of source names for the pci commands in testbios maks it hard to do a comparison without translating them to symbolics first.