I just tested at home, and I was able to reproduce something similar, and I figured out what's happening.
It boils down to the fact that I am casting strings to ints and vice-versa in a very stupid way, and in a way that I didn't consider that when I convert something like "030" to an integer, it will look "30", and once I convert it back to a string, it still remains "30" and in the code I am expecting the string to have 3 digits at all times, but when it doesn't, this bug happens.
The only turnaround for now is to set the MinCountdownTime to "100" or higher, and MaxCountdownTime to any value higher than that (it doesn't matter which).
As long as the first digit configured is not a zero, it will run fine.
The only way to properly fix this would be to compile a new package, which I would do so if it wasn't for the fact that you need to change a couple of stuff in another ini so it loads the fixed package instead of the broken one (as you cannot properly update a package without changing its name... I wished that Epic had looked a bit ahead and had at least assigned version codes to the packages to avoid mismatches, like Android does... but I digress).