Sounds to me more like something is causing a prolonged delay rather than it simply not running. Whether that's caused by the script or not is something that can't really be known without seeing the script.
Using clear all instead of clearvars is typically not necessary and can lead to slowdowns
... though I'm not sure if that command is normally part of your script.
Depending on how graphics objects are created, it's possible to have race conditions that may be caused by an object not existing before it's existence is required. The consequences of such a scenario depends entirely on what the code is doing.
