Thanks for the feedback.
Can you create a simple script that reproduces the issue for you?
For example, you say that your current script uses an alias to cycle through nicknames in the channel you are on, creates a timer for each one, and then that timer does something?
Can you create a simplified version of your script that reproduces the issue? Such as a simple, short alias that performs the above, based on your current script, and at the end it does something, for example, an "/echo" that displays a message for each completed timer. This should tell you whether it is completing its task or not.
Debugging a script, and tracking down the precise cause of an issue, is a really important part of programming/scripting. It is usually the only way that an issue can be tracked down and fixed.