Natobasso,
I felt that using Unsanity's 'fruit menu' and 'clear dock' which I love, might be the problem because on some forum there was a warning that the APE (Application Enhancer) can cause odd behaviors. This original annoying start up behavior had grown to: also not being able to access the sharing sys pref and not being able to mount the G5 on the G3. Disabling temporarily the APE immediately solved those problems, but the start up difficulty continues, APE disabled or not. I am considering uninstalling the ape altogether because of the other improvements but have not.
I have also just repaired permissions after the above as you have suggested.
I can Go/Connect at will now but I can only start up the G5 if I disconnect the ethernet and plug it back in after startup.
To be more specific, The G5 will start up, but before the drive and the finder are able to mount the connecting to G3 permissions screen pops up. It is not accessible due to the spinning beach ball. I have to use the reset button to restart. I have found another person with this problem on the Apple forums. The suggestion there was look for aliases for each machine on either machine. I have no aliases that I can find.
thanks