MAC OS X version 10.4.6.
4 x 2.5 GHz Power PC G5
Catalyst V4.01_m38

I have tested this with the server we have in our Service lab as well, and that system is 10.4.6
Dual 2.7 GHz Power PC G5
Catalyst V4.01_m38

Since this problem is difficult to visualize I will illustrate what I am doing step by step.

In the Cue List window, after making a few cues, I click on the time code under wait time to open the edit box.
After entering my time code numbers, I close the edit box by pressing enter.
The changes are saved correctly on all cues.
I then, simply close the cue lists window,
The time code edit box stays on the screen somehow.
This problem is almost always consistant.
I will go in manufacturing and test this on the new servers as well.

Like I said, it isn't causing any issues with playback. It is an annoyance.