Thanks for the suggestions, I tried every combination I could imagine regarding the NueBattery settings that I could think of with no change in the charging problems.
Some brief background:
Our family has 3 TP2 phones, all using custom ROMS and several mini usb chargers, the problems are present with all of the devices (e.g. it is not a cable, broken charger, lint on the connectors etc...) and have been present only on certain custom ROMS beginning roughly Nov or Dec 2010. Flashing any of the devices with the stock Sprint or an unaffected custom ROM immediately fixes the charging problem on any of our TP2 phones.
With your ROM, the phone will charge (as indicated by an amber light glowing to the left of the phone speaker) anytime the device is powered down. When the phone is powered on it will only charge when tethered to a computer or when using "better" chargers including the HTC wall charger and cable or some car chargers designed for older blackberry devices. Other mini usb chargers when plugged in bring up the dialog allowing you to select activesync, disk drive etc.. but will not charge the device regardless of which function is chosen. No charging occurrs even if the device is left connected to the charger for hours and the device will continue to function on battery power until it powers off and then finally will charge.
When on an affected charger and the device is off, the amber charging led is on. Using your ROM, when the device is powered up, the amber light goes off as the device boots but the charge light comes on approximately when the HTC logo screen switches to a windows phone screen. The amber charging light turns off a few seconds later while your shark boot screen is displayed. This suggests to me that the device begins charging appropriately and then a driver loads during bootup that causes the device to not charge when using certain chargers.
This seemed to be verified by member vin255764 in this post:
http://forum.ppcgeeks.com/2014458-post9274.html
"vin, i agree with other poster.. latest pluto doesnt seem to charge from the wall charger. i have 3 days before i go on vacation.. if its not fixed by then , i would have to go back to older rom.. coz i am not taking my laptop with
I was prepaired for this.Try to install nue% cab (few posts up),soft reset.
Go to start menu>settings>system>remove programs and remove this cab.Original module is in ROM.I think it will fix your issue "
For me, this fix got rid of the charging problem but I have tried installing Nuebattery and then removing it on other ROMS and it has no effect. The subsequent "Vindows" ROMs currently seem to be the only ones that do not have this charging issue for me. I love the ability to change and update my phone by flashing and would like to have the ability to try out all of the availabile ROMS without having to worry that I won't be able to charge the phone.
Thanks again for your ROM and for any help you could provide for those of us affected by these charging problems