hi steve, if the software cannot generate reasonable results with your manual time step it will override them.
just to double check things are working the way they should, setup a really simple problem (flow in a pipe maybe) with flow flowing constantly. get the steady state result and then turn it into a transient. then go to manual time step. since the problem is simple and time step isn't critical, you should see it use the manual time step.
the other time it may change is if you have periodic saving turned on that is smaller than your time step. but it sounds like it is using automatic time stepping.