I assume that you think the problem is with Ancestry.com via the updating that is done on FTM. You can change your frequency of updates or disconnect the computer from the internet to test this. FTM will run without the internet. If you still experience the same problem, it is likely your machine. You can try to see your resource usage (processor and RAM) through the task manager. It may also be another program you are running (perhaps even in the background).
If you want to eliminate any possible conflicting program, run it in safe mode.