Hi Brian,
AE-L is Auto Exposure Lock. Simply put, with AE-L on, you can press the shutter release down about half-way and the exposure you have in your camera's setting are locked on. You can move your gear around the area and still maintain the exposure you have set. Works the same way as Auto Focus Lock.
I still suspect the problem was your battery. I say that because you had stated that when you switched from Auto to Manual, everything functioned perfectly. Keep in mind that anything you have employed in your presets, i.e., Auto this and Auto that are a huge power drain on any battery. Also, anything such as Lens Correction or Distortion Correction are also power drains on the battery and especially in inclement weather, the batteries are strained enormously. Take the time to examine what you have in your camera's presets and determine what is necessary and what isn't. Of course, what you determine to be unnecessary, you can take it off of Auto. Also consider Highlight Correction and shadow correction. Yup, these can be and usually are the culprits that will kill your battery and slow all of the other functions down. Here is one way to test your battery. Take a photograph, then immediately look at your rear screen and see if the image takes an inordinate amount of time to appear. If it does take more than a nano-second, it is your presets. Let us know how you do. I hope this as been helpful.
All the best, Tony