Is there an IC that can charge multiple NiMH batteries at once?
From the LTC4011 datasheet:



Based on this, I think that the charger IC determines the average single-cell voltage input and uses that as a basis for how much current to charge with. So if you have a dead battery and a 100% battery connected in series, it would detect 50% voltage and charge at a normal rate, therefore damaging your fully charged battery. 

Further it states in the datasheet at the bottom of page 22 that "charging parallel cells is not recommended". So it appears this IC was designed with only one battery pack in mind. If you are looking for something that will charge multiple batteries separately, you might have to use a multi-port charger from HobbyKing or something, those will typically run you > $50 USD based on what I have seen searching the website.