Stroke mask circle logo reveal issues

If I understand your project correctly you have a bunch of masks with stroke applied that you are trying to use to reveal another layer. It sounds like you have multiple copies of the Stroke effect applied to the same layer. I suggest that you only use one copy of the Stroke effect and select All Masks and Sequentially. Set the Paint Style to Reveal Original Image, and set all masks to None. 

If you are just drawing circles to use as a matte for another layer I would use a shape layer instead of masks and the stroke effect. You've got a lot more options.

The only other option is to put each circle on a separate layer, animate each circle, then pre-compose them all and use them as a track matte or apply multiple copies of Set Matte to the layer you want to reveal. 

You need to educate yourself about mask modes and try to learn how to structure your work by pre-composing to isolate individual processing steps. trying to do everything in one step on one layere rarely ever gives you the results you may want. Some effects have specific requirements just like the internal pipeline has a specific order in which masks, effects and so on are processed under what conditions. A short excursion to the online help and reading up on this stuff is strongly advised. This stuff can't be understood intuitively, at least not in a simple and immediate way (things would only "click" eventually if you did this a hundred times and failed every time).

Mylenium