Yeah, it sounds like you didn't mix it thoroughly enough. Some RTV Silicones come with a coloured catalyst so you can tell how well you have mixed it in.
Two part mould is one way but a bit more time consuming.
Here is a youtube video showing out to mould a piece similar to the ones you want to do in a single part mould.
http://www.youtube.com/watch?v=7pEgH...2C1B280F377651
The video is advertising a particular brand of silicone and resin, but the principle is the same for which ever brand you use. Hope it helps.
Al