It sounds like you have a program that is scheduled to run at start-up but is not
What I would suggest is to check the list of programs scheduled to start at start-up to see if any are not in fact starting at start-up. There are multiple progams; i..e Windows Utilities that can tell you which programs are scheduled to run at startup. I like Slim Computer (free) the best for this. WinPatrol is also good. MSConfig will also list start-up programs but I have found it to be incomplete.
After you know which programs/processes are scheduled to run at start-up you can use Windows Task Manager or a free third party program like Slim Computer or System Explorer (I prefer System Explorer, which is free, for this) to see which programs/processes are in fact running.
Then just compare the list. Just make sure you do not manually start any programs after you reboot except for the program's you use to check which programs/processes are scheduled to run at start-up and which programs/processes are in fact running after start-up
You can also look at the applicable Windows Event log if you have turned on. It should give an error message.
I would highly recommend checking the progams in start-up once a month at a minumum, especially if you are installing and uninstalling progams. Too many progams today have click through programs that install with the program you are trying to install and very often the user is not aware of it. In fact to be really cautious I would recomend checking the start-up program list each time after you install a program using a program's installer, as opposed to updating through the program's GUI