If your maker has a dough setting try that, see if it comes out mixed up correctly, it will help resolve the problem perhaps by eliminating one. Your blade would cause this type of problem if it was not an evenly mixed dough.
As far as the yeast and salt, as correctly mentioned they need to be kept apart until mixed - yeast is killed by salt. When they are mixed together the level is relatively low due to all the other ingredients but if placed directly together it simply kills the yeast. It will do no harm other than your rise will be poor.
I always weigh my water. 1ml is exactly the same as 1g, its no coincidence 1ltr is the same as 1kg (1000ml / 1000g)
Try the dough setting, as long as it is evenly mixed and 'silky' and ever so slightly tacky it is mixing fine and you can start the process of elimination?