Hi Florian,
For a MIMO system, allmargin computes the margins of each loop with all other loops are closed. However, the command margin(-ol_sys(1,1)) doesn't know about any other loops.
Consider
load ol_sys
s = allmargin(-ol_sys,Focus=[0.001,inf]);
These are the margins at the first input with the loop closed on the second input (don't know why they are slightly different than your result)
s(1)
Manually close the second loop
L = feedback(-ol_sys,diag([0 1]));
and compute the margins on the first loop
allmargin(L(1,1),Focus=[0.001,inf])
which yields the same result as above.
margin(L(1,1))
