what seems to be the problem, have you done in btb, the xpitin,xpitout (checked flag icon), makes sure the xpitin.xpitout, doesn't run onto the main track,or it won't do the pit.
if you get black flag,that usally means the xsectors are facing wrong way.goto into btb and and click the (link track icon) and break it,rotate it,and relink it.