I'm on the latest version of Vpinball (10.2), but this issue was persistent with all previous versions too.
It also happens on other games launched through PinballX. For example PinballFX, Propinball, Future Pinball, VPDX_9, VPhysmod etc.
When launched directly without the use of the front end all is okay.
I have a USB keyboard, but play with the IPAC connected to a USB port. Both have been switched around to no avail.
Even tried with only a PS2 keyboard, same result.
Remapping keys no luck either.
Updating to the latest BIOS didn't matter either, but that was to be expected.
Last resort is always a format C, but I'd rather not.