I've given detailed descriptions of how the align sequence works before so won't retype it here, but not enough information from you to give you a solid answer.
If it was the align switch failing, it would normally keep moving until it overtravels (direction depends on whether signal failed open or closed).
What does (or doesn't) the axis do? Have you recently changed anything (like the motor or coupling)? Have you changed the hard drive or has anyone modified settings? Does the machine have the optional scale feedback on the Z-axis?
If you've changed anything on the axis recently, could just need a longer seek move.
If scale feedback, likely in the scale or reader head, but have seen the cables fail too.
If the hard drive was changed, several settings can cause an align failure if they are not correct.