It has been some time sonce I've worked with this widget, but I believe it has to return a 'true' value in order to keep running. Are there ways within your Microflow that might return 'false' as an output boolean?
Rochus is right. The microflow needs to return a 'true' value in order to keep on going. I did have a look at the code and cleaned it up. Version 3.0.0 is going to be released this week. https://github.com/mendix/MicroflowTimer/releases/tag/v3.0.0