A good answer is already provided by @canadianer, but as with many things in biology it is important to keep in mind what organism and/or cell type we are talking about. Because the nuances of the answer to a question about a seemingly universal process sometimes actually depend on whether we want to know about bacteria, or fungi, or mammalian stem cells, etc.
So I think the answer to your question is that synonymous codons are not always interchangeable because of what @canadianer described, but regulation of codon usage is probably more relevant in context of prokaryotes.
For example, for sure availability of a particular synonymous tRNA can be rate limiting in protein synthesis in prokaryotes, but I actually haven't heard of this happening in a eukaryotic system. If there are demonstrated examples, please paste it in the comment..
Also, the secondary structure of the coding part of mRNA is probably less important in eukaryotes, since they have a multitude of ubiquitous RNA-binding proteins that practically coat mRNA (e.g. hnRNP in the nucleus, and probably something similar in the cytoplasm, too)