Brian,

In response to your actual question. When I used Nicads I would often charge while driving. It has been my experience in most cars that there is a voltage drop and surge when you turn the ignition to start the car. It is possible that this could damage a charger but it is not a high risk IMHO. The real problem is that the charger will normally reset during the ignition from the drop in voltage. Thus you must start the charge cycle after the car is running. Also if the car does not maintain a relative stable supply voltage you may get false peaks or other problems. The higher voltage while the engine is running will not hurt the charger. In fact it is required in chargers that have a voltage bosting circuit to allow charging batteries over 12V. The case that is most likely to damage a charger is when the car battery voltage falls to low and the charger get damaged from low voltage. However most modern chargers have a reasonable low cut off voltage programed in that protects the charger.

Why don't you get a cheap PC power supply (~$15) to power your charger and charge you batteries at home? Take a look at the instructions on the bottom left hand side at this site, http://www.rcbatteryclinic.com/ or search for instructions at this site.