From where are these callbacks called? Is handles the current value of the handles struct or does it contain the value of the struct as it was during the creation of the callback? The debugger will tell you this, simply set some breakpoints and check the contents of handles.
A solution is to get the current value of the struct at first:
function hpos(hObject, pos, handles)
handles = guidata(hObject);
handles.A.L{handles.im}=value1;
guidata(hObject, handles);
function hpos2(hObject, pos, handles)
handles = guidata(hObject);
handles.A.R{handles.im}=value2;
guidata(hObject, handles);
Or maybe another callback is responsible for resetting handles.A unexpectedly? Again the debugger will help you.
