First I will invite you to post you code that exibits this behaviour.
Second I willv enture a guess that all of your functions are in a single VI that is set for "Time-Critical" and the "wait" you are using is a "wait until next millisecond...". I venture this guess because you have described exactly what will happen
when a "wait unitl..." is encountered in a TC VI.
If this guess is correct, you have to move the other functions to another VI so they can execute while the TC loop is sleeping.
Trying to help,
Ben