As PKR said this is not a matter of the old charge level memory effect NiCad and NimH batteries suffered from, because onwards from now we deal with Li Ion batteries which don't require to be fully discharged to be charged again, as long as you've offered them the proper full charge/full discharge cycles when new.
This is a matter of how the chip which is inside the battery circuitry "talks" with both the charger and the camera firmwares.
Installing chips in batteries is a trick used by cameras (and all other electronical devices) manufacturers to lock things out so that you must buy OEM spare or new batteries.
Using third party batteries can expose you to such problems, mainly the one you had to face when in Italy, that is, a fully charged battery detected as an empty one by the camera firmware, and a camera which won't want to switch on.
The M9 belongs to the most expensive digital cameras available, so trying to save a few pennies on no-name spare batteries can sound a bit odd, especially when traveling in a very nice place where a large amount of photos is expected to be taken.
For my D700 I am using a set of two original Nikon EN-EL3 batteries. Actually the D700 is a great energy saver and one battery only was enough for one week of shooting in Italy and two 4GB cards filled with NEF files.
You can try to set the M9 custom settings so that energy will be saved to the utmost (set the rear LCD luminosity down, limit the reviewing time to 2 seconds, disable all the useless bells and whistles, don't shoot in C mode, and resist the temptation to always look at the photos on the camera screen with many zooms-in etc etc).
