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I have a table where I let the users select records and then use this selection to "drill" to another report (open another report and use the selected records as a filter)
The action to open a drill is in a context menu, which opens when right clicked on any record.
Is it too confusing that the selection gets used for a drill and not the record where the user has clicked right?
To quote Microsoft: The [context] menu items should apply only to the selected (or clicked upon) object or window region.
The selected records are still selected objects. You should make sure that the context to which the menu applies is clear.
A good example is Firefox context menu that appears when you right click within an iFrame - it shows actions related to the page and an extra item called "This Frame" to show extra actions in the context of the frame:
Therefore, I suggest you change the item name from "Drills" to something that better indicates the context - for example: "Selected Records".
Your attribute "Selected" being checked is not to confuse with a row in the list being selected, or focused, for an upcoming action, like open (enter), delete or for actions from a toolbar. Let's dub this "list selection" for the moment. This is how you select for example a file in the Windows Explorer or Apple's Finder. You may do multiple list selections by holding shift or ctrl/cmd.
What you right click on is always the subject of the right click context menu. Do not put actions for any arbitrary record in the context of a another record. That way you would mix up the contexts.
For example, In Windows Explorer, the list selection even changes when you right click, to emphasize what context the context menu performs its actions on.
I would move your drill actions for sets of checked items to a toolbar next to the list, like for example Gmail does, and only keep them in the context menu if it makes sense to perform them on the list selected item or items.
