Slider on Master Slide Disappers

I have a course (cannot upload any slides due to security reasons), where I use the slider to show the learner his/her progress through the course. The slider has 5 stops, and each stop is labeled as Section 1, Section 2, Section 3, etc.  I inserted the slider in one of my master slides, and that Master Slide has 5 layers (1 for each slider stop). The visual differences between each layer shows the learner his/her progression through the course. When the learner is in Section 1, the Slider is in Stop #1 by presenting Layer 1. When the learner is in Section 2, the Slider is in Stop #2 by presenting Layer 2. Etc. 

I've used this template successfully for 5 courses, up to now. I am finishing a new course, and this time, I am showing a couple presentation slides that have a couple layers. The first slide, the slide automatically transitions between the layers when hitting the cue points on the time line. The second slide, the user clicks on a shape to bring up the layer and additional information. My problem is that when I am using the layers on the Presentation Slide, I am losing the Master Slide Layer, which shows the learner which section he/she is in. The Slider Stop only is showing while the base layer is showing. 

Any ideas why this might be occurring and potential fix? 

Again, would love to upload the Slides for you, but due to security reasons, I cannot.

Thanks for any ideas.

Jeff