According to Wikipedia, PVRTC has the following limitations:
- Height and width must be a power of two.
- Must be square; height is equal to width.
- Height and width must be at least 8.
Did you export your atlas textures to fulfill these three requirements?
Also check if PVRTC is the right compression for you.
Depending on your sprite style, its compression artifacts can make clean sprites unacceptably dirty. You don't want to go through all the trouble making all your sprites compressible only to realize that it doesn't suit your needs.
