The command script may be timed out due to how it works. Not knowing how it's written exactly, but to me it sounds like the script searches the whole route for destinations. When commands do that, they cause a major timeout and stutters that cause poor performance. Since TANE came out, scripts that do that, such as Wait for Trigger, are prevented from executing.
If the script can be edited, perhaps someone who is capable of editing the script, and also has permission to repair the asset to do so, can fix the problem.