I’m aware of the age of this thread is quite old but I wanted to comment.
I can’t believe that people are actually stating to never use silicone bakeware that it is so poor to use and so on.
You call yourselves bakers?
True bakers are creative at heart and will learn to work with different mediums.
If Silicone bakeware is soo poor then how does one of the best Chefs in the world use it so much? Chef Amaury Guichon. Look him up he uses all kinds of custom silicone bakeware.

I found that silicone baking items steam baked goods leaving them mushy. I stopped using the few that I bought for that reason.

I have silicone mini pie molds but they didn't send no baking instructions.

What tempature do you bake mini pies and how long?

Silicone molds are not ideal for baking. I wanted to make some cupcake hearts and the time it took to bake them was at least doubled. The small silicone shapes are good for hard Christmas candy.

The only thing I have found silicone bakeware is good for is for molds. I have found some for making different sized bars and other different shapes that I use to mold anything from chocolate to duck fat. I use the bars for duck fat and roux for storing or traveling with.

Yes, it does take longer because silicone is an insulator. I wouldn't increase the oven temperature but you will need to bake them longer. Then, give away the silicone bakeware!

As I'm sure you've figured out by now, yes silicone bakeware will take longer. I stopped using mine for pretty much that same reasons as betteirene describes. I hope your cupcakes came out okay!

When baking with a material that does not retain and conduct heat, you will indeed need to make adjustments. There's no nice, neat formula for those adjustments--increase both the time and the temperature by slight amounts, keep your fingers crossed and hope for the best, and if it works, write it down so that you can duplicate it next time you bake cupcakes.

Try not to purchase bakeware made of silicone (or tin or thin aluminum) ever again,

I love my silicone spatulas because it's almost impossible to melt them. Silpat, the brand name only, silicone pan liners are wonderful for certain applications, such as baking lace cookies. Silicone oven mitts are okay. Silicone whisks, maybe. But silicone bakeware? If it's not too late, try to get your money back.

http://www.food52.com/foodpickle/2873-i-used-silicon-muffin-pan

Difficult to answer. However most recipes and heat requirements are designed for metal 'muffin pan' with paper inserts. Heat transfer in metal can vary--some recipes list higher temps and time for non-stick pans vs older metal cupcake pans which are darker in color after use. Silicone is still realtively new for baking. IMHO I'd stick with metal...and personally, for cupcakes. I enjoy the peeling the paper cup on the cupcake as a hand-held serving device.