I've never used the Wait Until... command within a Schedule Library schedule but the regular wait command works fine. This may or not be a bug.
Your best bet is to put the Wait Until... command external to the Schedule Library schedule and insert that in the driver's command bar.
Remember, you need to use the Copy Commands from command to insert the Schedule Library schedule into the driver's command bar. When using the Copy Commands from command, always use the Insert Schedule. The other options don't work as intended and the schedules will be messed up.
Keep in mind is the repeat command can't be used within the Schedule Library schedule. The original author says this in his documentation.
Insert a wait... command in between inserted multiple Copy Commands from commands. This is something that's mentioned in the documentation as well. This will give the commands a chance to load. I have found putting a Wait... command at the beginning of each driver schedule also helps in this regard. A wait time of 20 seconds works perfect for the in between ones. The initial wait time can be however long you want to make it.
As far as other tools for generating schedules, I don't think there are any available. scheduling has always been a weakness with Trainz unfortunately. We may be lucky with the new Trainz Living Railroad once that's fully implemented.