I think almost every map I've posted so far has water at higher altitudes than 0m. And I've made lakes at considerable altitudes .
You may have to adjust the settings when/if you work on the original grey/color files in Microdem. To get water at altitudes, you need to 'uncheck' the sea level and lake check options. Otherwise it seems that all water is pushed to 0m. Which then results in lakes that would have been at say 200m altitude, being set at 0m, which gives very steep sides to the lakes ...
The thing with lakes at altitude though, is that you cannot ake them with Microem. They have to be imported somehow or another into your grey value map. You can do this by hand - sometimes the lakes are visible as same colored RGB grey values. Then you click them with a magic wand tool at 0 tolerance, and create a separate grey map that you later convert to my_mapC.tga.
You do that with all water and river systems, creating them by hand by carefully following river beds or lakes in the grey Microdem map.
Sometimes you can also import a lake or water body layer from a Google map layers site
http://www.maps-for-free.com/
but then you have to downsize/upsize the imported layers to a pixel perfect match. Works well for small amounts of lakes/rivers, but with intricate systems you're better off doing it all by hand, even if it does take a day or two of full hours to get some of these areas done. The Hankow, Madagascar, Mozambique maps for instance were real doozies in the rivers department. They never seemed to end.
That's also why it's fun to make desert maps ... ha ha