What do you mean the secondary DVR is turned off? Do you mean that it is just put into standby, by using the power off button on the remote, or on the front of the DVR? Or do you mean that you unplug the power cable, or turn off a power outlet that it is plugged into?
If the DVR still has power to it, then it is not truly turned off. It is just in standby, and it can still receive the instructions to record programs etc from the website.
If you are actually killing power to the DVR then you are correct you won't be able to set recordings from the website. I'm wondering if this is actually your issue, and the names of the DVRs on direcTV's website are just backward from what you actually have set up in your home (for example the one on the website labelled as bedroom is actually in the living room at your house, and the one labelled on the website as living room is actually in the bedroom).
Look at the actual model numbers of your two DVRs (HR21-700, HR24-500, etc), and which rooms they are located in, and compare that to what DirecTV has in their system at the website. If both of your DVRs have the same model number then you need to look at the receiver ID numbers.
Also, if you can post your model numbers on here we may be able to give you more help if there is some other issue. For example I think at one time the HR34 couldn't be programmed from the website, can't remember if that is still the case or not.