If cells in series are mismatched in capacity, will the capacity tend to even out?
In general, if you have cells with different capacity in series, the lower capacity ones will discharge faster. If you put a AAA and a AA in series and lit up an LED, after a while the AAA would be at a significantly lower voltage than the AA. 

AA cells are relatively well matched in capacity and output impedance, but there certainly can be differences based on the manufacturer. Some of the cheap ones use different chemistry and have lower capacity (zinc), so if you mix them with higher capacity cells (alkaline) in series, they will discharge unevenly.

If the cells in your remote are made by different manufacturers, or are in different stages of discharge/use, you may end up in a situation where some of the cells are 'dead' (have a prohibitively high series resistance) and some can still be used. Unless you put all the cells in the device 'brand new', you don't have a legitimate basis to assume they're all dead once you see the message. 

Why don't you pick up a cheap multimeter and see for yourself? You don't need anything crazy, a $10 multimeter would do.