The "WaitBeforeCheckSecs" property is a simple buffer time between the when your form is created and the when the AutomaticUpdater begins checking for updates. This is meant to be a low number (e.g. 10 to 30 seconds). And the checking should fire only once.
It sounds like you're using the "WaitBeforeCheckSecs" property to wait a long time before checking. If this is the case then you're probably better off setting the "UpdateType" to "DoNothing" and manually checking for updates when you need to. Then, just before you've started checking for updates, set the UpdateType to "Automatic".
Does this help?