Mike, Not guaranteeing this is your issue, but you are describing a fairly classic symptom of a 2-hour offset in a resource calendar compared to the default project time assumptions. I can get exactly the symptoms you describe by creating a default project, adding two tasks in series, and assigning a resource whose working time is 06:00 to 15:00 rather than the default 08:00 to 17:00. You need to set your options to show clock time to see this.
When I first create the project, the software sets the project “Start date” to 08:00 today. Any changes that I make to the schedule settings (e.g. changing the standard start-finish times from 8-17 to 6-15, etc.) do not apply retroactively to this project field. Consequently, my resources can’t start working until 08:00 on the first day, go home at 15:00, then come back at 06:00 the following morning to finish the last two hours of their first “day’s” work. This 2-hour offset cascades through the schedule. Once I manually correct the project “Start date” to 06:00 today, 8-hour workdays are restored.