Ok so if you go to the Pre-Capture options, you will see for the Auto Capture Timer, you can tell it what kind of capture to perform; if you select "Repeat Region", it should always be capturing the last region you selected for capture.
I think that's what you want -- so it will always be grabbing the specific region you first selected.
(Don't engage the delay, that's different from the Auto Capture Timer).
Let me know if that works for you!