Why won't my Nikon D40 stay in infra red remote control mode, trying to take wildlife shots, have to wait for right shot but after about 1min. remote does not work?

When you switch the camera to the remote control logo on the main dial, the camera expects a infra red remote control. I don't think when you use a wired remote, it should be in that setting.
Try one thing at a time. First try to release the shutter with the push button on your JJC, when the camera is in the normal setting S (single shot) Be aware if you select Bulb, the shutter stays open as long as you press the button. If the your camera reacts when pressing the JJC, then do your settings on the JJC for the more complex things you want. Still I think what your JJC can, the camera can do too without JJC. But not sure of everything you have in you'd head.

Success

Clean the contacts on the camera body lens mount with a cotton swab lightly dampened with rubbing alcohol.

Hi,
You might be shooting with a higher ISO or in settings where the D40 meter finds enough light and doesn't activate the flash.

Try changing the ISO to a lower one, like ISO 200 and take some test shots indoors, in a darkened room.

OR, you might have the mode dial set to "no flash". That's the crossed out lighting-bolt symbol. Just set it for P or another mode and you're back in business.

Hope this helps

Pres the "+" button once, look for Shooting modes. You will have the following options:

• Single shot (S)
• Multiple shots
• Timer
• Remote control
• Remote control 2s

With Remote control, the camera will take a picture when you press the remote.
With Remote control 2s, the camera will wait for 2 seconds when you press the button and after that take the picture.

Set the exposure mode to Manual (M) or Shutter-priority (S) and specify the shutter speed yourself. You'll have to set it sufficiently slow in order to see any difference between front- and rear-curtain.

Set the release mode to one of the two remote modes. Quick-response takes a shot immediately, Delayed-remote waits two seconds, giving you an opportunity to hide the remote control behind your back.

You probably have "bracketing" turned on. In your menu settings, search for bracketing and make sure it is off.

Why not invest in Nikon's Camera Control software.  When the camera is attached to a laptop, you have complete control of the camera from the computer, and it will do time-lapse shots at any interval you choose.

Is the lens moving/focusing?
If you switch to manual focus, can you make a shot?

Is it possible that "remote control" mode is selected (the button on top, right, in front of AF button) - in this mode the camera focuses but waits for the remote to shoot - just press the mode button until the LCD shows [S]

read manual ! you can change it up tp 15min.

Find in Custom Settings > "17 remote duration".
if it is not there change first in SETUP MENU>CSM/Setup menu from "simple" to "full"