Testing here, I can confirm the same problem. It's not a udev thing. On base, try loading pilot-link-base.tcz and then:
pilot-xfer -p usb: -l -t 5
I get christmas, same error as netnomad.
The problem is either in the pilot-link extension or in libusb. I'm tempted to think I just need to rebuild/update the pilot-link extension, otherwise I'd expect libusb problems all over the shop.
I'll test some more as soon as possible, but it could be a few days. Sorry to keep you waiting!
EDIT:
Umm ... maybe not in pilot-xfer after all. The connection works if I sudo pilot-xfer, but that won't be a solution - pilot-xfer is called by Jpilot. The pilot-xfer binary is tc:staff. Changing pilot-xfer to root:root in the extension (reboot/reload) doesn't solve the problem, and it must be connecting to libusb correctly (or there wouldn't be a connection at all, ever).
I'm stumped for the moment, and it's 1am here. Time for bed!
EDIT: Okay, didn't go to bed. Permissions on /dev/bus/usb have changed between 3.8 to 4.0. Using base/norestore:
ls -l -R on /dev/bus/usb for 3.8.1:
/dev/bus/usb:
total 0
drwxr-xr-x 2 root root 60 Oct 9 00:14 001/
drwxr-xr-x 2 root root 60 Oct 9 00:14 002/
drwxr-xr-x 2 root root 80 Oct 9 00:14 003/
drwxr-xr-x 2 root root 60 Oct 9 00:14 004/
drwxr-xr-x 2 root root 60 Oct 9 00:14 005/
/dev/bus/usb/001:
total 0
crw-rw-r-- 1 root staff 189, 0 Oct 9 00:14 001
/dev/bus/usb/002:
total 0
crw-rw-r-- 1 root staff 189, 128 Oct 9 00:14 001
/dev/bus/usb/003:
total 0
crw-rw-r-- 1 root staff 189, 256 Oct 9 00:14 001
crw-rw-r-- 1 root staff 189, 257 Oct 9 00:14 002
/dev/bus/usb/004:
total 0
crw-rw-r-- 1 root staff 189, 384 Oct 9 00:14 001
/dev/bus/usb/005:
total 0
crw-rw-r-- 1 root staff 189, 512 Oct 9 00:14 001
ls -l -R on /dev/bus/usb for 4.0.1:
/dev/bus/usb/:
total 0
drwxr-xr-x 2 root root 60 Oct 9 00:13 001/
drwxr-xr-x 2 root root 60 Oct 9 00:13 002/
drwxr-xr-x 2 root root 80 Oct 9 00:13 003/
drwxr-xr-x 2 root root 60 Oct 9 00:13 004/
drwxr-xr-x 2 root root 60 Oct 9 00:13 005/
/dev/bus/usb/001:
total 0
crw-r--r-- 1 root root 189, 0 Oct 9 00:13 001
/dev/bus/usb/002:
total 0
crw-r--r-- 1 root root 189, 128 Oct 9 00:13 001
/dev/bus/usb/003:
total 0
crw-r--r-- 1 root root 189, 256 Oct 9 00:13 001
crw-r--r-- 1 root root 189, 257 Oct 9 00:13 002
/dev/bus/usb/004:
total 0
crw-r--r-- 1 root root 189, 384 Oct 9 00:13 001
/dev/bus/usb/005:
total 0
crw-r--r-- 1 root root 189, 512 Oct 9 00:13 001
And I'm going to bed. For real this time.