ProjeX only uses the dependencies for the actual Gantt
plotting if you tell it to in the 'Display Parameters'
dialog.
When you do the reset it sets the default for using the
dependencies back to off. Under the General tab of
'Display Properties' there is an option to 'Use
dependencies for task start dates'. Select this and it
will use the dependencies you have set to draw the Gantt
chart and also, when you bring up the 'Set dependencies'
option, by default the 'Update using dependencies' box
will be checked.