I have found the bug with the cut off vertical terminal scrollbars ;-) and the fix is really easy, only a single line needs to be added to vte.c, I found this by comparing with the Anjuta source..
ok, so vte.c, line 151 says:
vf->vte_terminal_set_size(VTE_TERMINAL(vte), 30, 1);
Just above this line, add the following new line:
gtk_widget_set_size_request(GTK_WIDGET(vte), 10, 10);
I have checked and rechecked, and I am pretty confident that just adding this one line fixes it. I even did a clean CVS checkout of the latest revision 987 and added just this one line and it has fixed the problem.