Any changes I make to the ~/GNUstep/Library/Afterstep/start/
hierarchy are erased the next time I start X.
I have verified this to be a problem. If you make the changes to the
start directory and then startx, the changes are removed and it starts
with a default setup. If you make the changes to the start directory
from an xterm and then just choose 'restart session' the changes are
left intact and the menu behaves properly.
That is because of the wmconfig processing that will take palce in
that directory. The start dir is created/controlled by wmconfig
In the 5.2 this problem was fixed by having the ability to create a
"fixed" dir on the same level with the start dir that will include
changes to the menu structure.