I don't know if this is a SSBB update. It is the fact that your laser had to adjust to read a Dual Layer disk vs. a single layer disk. This can definately cause skipping, as it is confused. An original copy can sometimes make it easier on the drive, but copies really can do damage. The other question to ask is how long have you spent playing SSBB. If you spent a bit of time with it, your laser is out of wack most likely.
Some of the things to consider is:
1- Dual Layer disks use different dyes then Single Layer
2- Different Brands between the 2 media
3- Burn speed is different if you followed the directions - SSBB 1x, other games 6x
Try putting in another single layer game and let it run for a while. Make sure it is the same burn speed and media as your GH customs. Then try GH again. See what happens then.
Also, if it is a song, it could be where the song is read on the DVD burn. Really a lot of factors. I don't think the SSBB is the culprit. I know this happen to people with rythm games on the PS2.
Now for my question, how can I tell if something is out of sync. Is it obvious delay, or just very minimal where you feel like you hit the correct note, but it doesn't register. Because I sometimes have that. It could be because I missed the note, but when I focus on hitting the next note, it always registers correctly. So do you mean in heavy areas it doesn't register, or all the way through.
The other problem I was having, only on Bobitos version was that the wiimote was not making the note miss sound. Could this be an issue of skipping? Bobitos, on your version, do you have it that the remote makes a noise when you make a mistake?