According to the Faiths of Faerun thread, the domains Shar supports are
* Knowledge
* Caverns
* Darkness
* Evil
If you make a cleric of Shar, NE, with Darkness and Knowledge, you get a message that these domains are not supported by the deity.
I double-checked to make share that Shar was typed correctly and that the domains are indeed Darkness and Knowledge. I also made sure to download the latest domains.2da before making the character.
I would guess that maybe in the game code, one of the domains, either Knowledge or Darkness, were omitted from belonging to Shar.
I had a similar problem that I was told to remedy by resting and relogging while having my domain power up, ensuring myself I had the proper domains. I would suggest trying that with the Darkness domain ultravision if you haven't already.
The information used by our deity validation script says that Shar supports any evil alignment, as well as those four domains.
None of these domains have activated Domain Power feats (which are different from items/tools).
However, the domains.2da indicates that a number of our custom domains should be castable feats (this feature would require a modified feat.2da file, I think). This may be causing the problem. I'll look into it more after dinner.
Just read the other bug report. Disregard what I said above.