[AT&T Samsung Galaxy S II Skyrocket SGH-I727] dgoby:
So I decided to go ahead and put my findings of this issue that several of us have had with our phones getting the dreaded "Battery Disconnect" after upgrading from stock ICS to stock JB. I cannot guarantee that this will work for everyone but it did work for me.

Here are the different solutions I have come across in my research on this issue.

1: Battery corruption: get new battery

2: Gold prongs are dirty on phone and battery: clean them

3: Bad charger: get new charger

4: Dirt or dust in USB port: clean with compressed air

Now I tried each of these and unfortunately none worked for me. It has for some that I have read on different sites, so if you don't want to try and re-flash everything try those above.

For those that have tried each of above 4 and still have the issue, like myself, you can try the following. This worked for me, but you have to have patience. Read entire post before trying, check MD5 sums before any flashing and the typical disclaimer, I AM NOT RESPONSIBLE FOR YOU PHONE, TRY AT OWN RISK. Sorry, had to put that in.

1. Have your battery charged to 100%. You need to go back to ICS if you aren't already. If you are on JB right now, wipe your system clean (factory reset) that's including formatting system, data, cache, dalvic, etc. using CWM (that's just what I prefer for this part and what I used). Do a backup first of anything you don't want to lose. I used Titanium Backup Pro myself but pick your own poison. If already on ICS, proceed to step 4.

2: Using ODIN, flash ICS back on to your phone. If you haven't already looked at Vincom's guides, here you go. http://xdaforums.com/showthread.php?t=1652398 and http://xdaforums.com/showthread.php?t=1785999. Keep it plugged into the computer while it reboots. Should show battery charging. If not, do it over. DO NOT ADD CUSTOM RECOVERY AND ROOT.

3: Test all your chargers. Generic and OEM and any additional batteries you may have. Make sure they all work. If so, let it settle for about 10 minutes and then on to the next step.

4: Power off the device and boot into the stock recovery. Do a factory reset, choose reboot and when the phone powers off, take out your battery.

5: Now using ODIN, flash stock JB. Again, leave the phone plugged into the computer until it boots completely. As long as it is charging and not "Battery Disconnect" you're on the right track. If it does not boot, basically just sits on the AT&T symbol for an extended period of time which can happen, remove battery, reboot into stock recovery, factory reset and re-flash JB again. If it says "Battery Disconnect" after it boots, wipe, and re-flash JB again. DO NOT INSTALL CUSTOM RECOVERY OR ROOT YET. I did on my first attempt of these steps and immediately got the "Battery Disconnect". If you succeeded, on to the next step.

6: This is when your patience comes to affect. You need to let the phone settle. I gave mine 2 days of using and charging when dead without getting the "Battery Disconnect". It happened once after a full charge, but only once. I plugged it in while half charged to see what happened and it popped up. Later when it died and I plugged it in, it charged with no problems. Patience. Something about the drivers taking time to settle either in the rom itself or in the kernel for certain devices. Not sure which. I did re-install my apps but I did with using the Play Store and not with my backup. Make sure you are on Wi-Fi so you don't jack up your data usage.

7: Now that you have had two days of using and charging with no issues, fingers crossed, go ahead and install TWRP using ODIN (no wipes needed). After it reboots, again keep it plugged into the computer and if it is charging after boot without the dreaded phrase, CONGRATULATIONS! BUT, I would wait for at least one day before you try any custom roms on it. Again, let it settle first.

I know this is a lot. But again, this is what worked for me after trying for almost two weeks now to find a solution. Good luck everyone, I hope this works for you as well. And thank you Vincom for the guidance.