Michael.
Answered your PM ... probably not a lot of help to you.
This is a nuisance I know, but can we step through the process, just to (a) be sure, (b) try to isolate the cause (c) help someone in future that might have the same issue?
I'm making the assumption that once you've programmed the DS, you remove the jumper from Pin5

?
This takes it out of 'bootload mode' to 'run my sketch as soon as I'm powered' mode.If we can verify the following.
1. Does a normal DS cause the computer to make a noise when its plugged in.?
2. Does the revised DS also make a noise.?
3. Does the revised DS make a noise if the jumper from Pin5 to ground is in.?
(means its accepted the new bootloader)4. Is the Pin5 lead/jumper/wire a good fit in the socket.? (A slight kink will help)
5. Is the slight wear pattern on the USB aligned with the gold pcb tracks.?
6. Is the wear present on all 4 pins.?
7. Can you program sketches into an unmodified DS, without any issues.?
8.
When the DS is present, what CommPort is it using.?A simple Yes/No unless it needs more is fine.
In the meantime I'll ask some questions about Vista, and why it appears to be so different.
Mark