Joel,
silly question, but there isn't any chance you've got two versions of gpilotd 
on your system: one that you run from the command line and one that the applet 
finds?  There aren't any arguments that I can think of that would affect the 
behaviour as you describe.

One thing to check is whether your /dev/pilot symlink always points to
the right ttyUSBx device.  I've a vague notion I've come across cases
where it sometimes gets confused, pointing to either ttyUSB1 or ttyUSB0,
but not consistently.  If this is the case you may want to try
configuring gpilotd to use the correct ttyUSBx device rather than
relying on /dev/pilot.  Either that, or configure pilot-link for libusb
syncing (search around for the howto) and then you can use the "usb:"
pseudo device.

-- 
After one sync, connections to a Tungsten T3 device fails
https://launchpad.net/bugs/67077

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