Ok. I've discovered that the auto assign for rehearsal marks has an unchecked box. This is easily fixed by clicking EDIT when the expression dialog box is open. Select the rehearsal marks category, select the first rehearsal mark (at this point they all look the same, don't worry), check the box for 'Use Auto-sequencing style:', select the appropriate style (cap letters, numbers, or measure numbers), click OK. If you repeat these steps but change the style to one of the other options for the other expressions they will appear in the dialog box as specified.
Let me know if this is unclear in any manner and I'll repost the steps with a bit more detail.
At this point, you should save the open file. If is a current file with some note already entered, just save and continue. If you want to fix this for future files use these steps but work with each of the templates. When you have completed the correction for a blank template, select Save As, navigate to where the templates are stored, make certain that you name the file exactly as it appears in the VDL template folder. This will replace the existing file but you will then not need to fix the problem with future projects.
Again, if anything is unclear let me know and I will repost.
Still working on the Title issue, but I think I know what has happened. The simple solution at the moment is to manually enter that information using the Title Tool.