It seems lately that we pretty consistently lose lock at CARM_TO_TR the first time we try after having done an initial alignment, and then regularly make it the second time.  We should look into what setting(s) we might be setting in initial alignment that we're not resetting properly until we try to acquire and then go through the DOWN state of everything. 

EDIT: Sheila points out we should check settings in the Xarm IR alignment area of initial alignment, since it's probably the most likely to be causing this kind of problem.