Ok I have a bit more information on what seems to be going on.

Launching the game from steam executes /steamapps/common/star trek online/star trek online.exe

This is the patcher. Once the patcher has done its thing, it appears to load steamapps/common/star trek online/star trek online/live/gameclient.exe
It is when the patcher launches gameclient that it loses the steam overlay, and with it my ability to buy cryptic points.

I could resolve the problem by manually launching gameclient.exe from steam, but when I do that I am unable to reach the account servers in game.

So. . . where do we go from here?