There could be a number of reasons why you are experiencing carbonation issues. Secondary fermentation is not one of them, there will be plenty of yeast to carbonate after secondary.
How are you carbonating? (What are you using as a priming agent, how long are you letting the bottles sit before opening, and what temperature are they at while they are carbonating?) If you can provide that information, we should be able to provide more assistance.
Make Beer, Not War.