I have not had any problems with the start menu. Like I said earlier, I make the xp version first on my other machine, install it on the Vista machine, etc.
Then I open the Vista version....in the start panel, I go to the extras tab, and set my margins for Vista there: the top and bottom bar I make the same as for XP. The left panels, I make them 230 px wide (my XP version is 190). I make the right panel 150 px wide (my XP version is 190). Works for me every time.....then I can proceed with tweaking the Vista version, and adding the Vista only stuff to the blind. If you have a weird shaped start panel, you may have to re-cut your start panel into the specific sizes for Vista, or you will have alignment problems. I had to do that with Scapolite.
For me, it is quicker building the XP version first, so that is why I start with it first.