You didn't specify which controller you're using but this behavior is common for timers. In general, timers will not function correctly in periodic tasks/subroutines. Timers need to be ran every scan in order to accumulate time properly. There may be exceptions to this but this is most likely causing the problem you're seeing.

I found an article about timers. I wonder if you are interested in reading it.

Sub routines have to be scanned to operate. if your wanting to execute something in the routine based on a time interval then use a counter triggered by one of the system clock tags then when the output on the counter is reached enable the routine until it is finished then clear the counter while in the routine. I use timers in subroutines all the time but have program control flags to exit the subroutine if the timer has not expired.