I already answered your support ticket, but I will place my answer here as well, so that it is available to all who might run into the same problem:
First of all, please make sure that you are using the latest version of the Prometheus suite, namely version 2007.3.1314.20.
I suppose the problem comes from the fact that at a certain point the TargetControls collection of the RadToolTipManager is empty. By default, when this collection is empty, the manager tooltipifies all elements on the page. You can add a simple check, whether this collection is empty, and in case it is, set the Visible property of the manager to false.
Taking into account such situations, we have added a new property to the RadToolTipManager - AutoTooltipify. This new feature will be available with SP2, scheduler for the beginning of next week. Therefore, in case you wait for the new version of the Prometheus suite, you will be able to just set the AutoTooltipify property of the manager to false.
the Telerik team