sometimes application variables don't reset

In our application.cfm, many queries are run and set to arrays that are application scope. They are for code tables. To keep all this from happenning each time a template runs, there is a server scope variable that is set to true from another program and in application.cfm, there is something like <cfif the server variable is true> run queries,assign arrays,set server variable to false  </cfif>.

When a new code is added to a code table, we set the server variable to true and the next template that runs resets all the application variables and the new code is in one of them.

Sometimes this doesn't work. Only some of the arrays get reset and the others are empty. The arrays are there but have no elements.

Repeating the process 2 to 4 times seems to make it work.

What can cause it not to work the first time ?