Don, this is priority 1 and really needs to be fixed. When a lot of peptides are selected, it can take minutes to show this graph. The code is not efficiently culling the list to get only the 100 most intense peaks. The code ends up pulling data for all selected peptides before realizing it will only graph 100.
I just spoke with someone here in Zurich who asked if there was some way of cancelling this display, since he clearly had regretted clicking on things that caused Skyline to appear to hang.