I was subscribed to Champions Online for a few months but did not use my monthly stipend (have around 827C). I decided to give STO another try. I loged into STO and see that I only have 27C. I use the same account for both games but I have 2 different C-point amounts. Did I miss something somewhere?

If you are a subscriber to both games, you receive 400 points for each game that you are subscribed to. The c-points that are stipends are on available in the game you receive the stipend from. If you buy c-points they show up as accessible in both games.

The discrepancy between the two different c-store amounts is related to the stipends amount from the different games and the different purchases made from each game pulling from not only your purchased c-store points but also from your stipend points.

Oh ok. They are all called Cryptic Points so I thought it was all the same. The same company gets the money no mater which game you spend them on. I assume when you purchase something from the C-store it uses your stipend before it uses your purchased C-points?

Only if you but the points out right can they be used in either game. If those points were given for something you did in a game it's game bound.

Yeah I forgot about the in game means of acquiring c-points. Besides the stipends that are game bound the c-points you receive in that game are also like Otakuboy stated.

Yes, if you buy something in either game, it should use up the C-Points that are bound to that specific game in your account first, before it uses global C-Points.