In PSoC Creator 2.1, the default Device Configuration Mode setting in the Design-Wide Resources (DWR) System Editor was changed from "DMA" to "Compressed." This causes the configuration data to be compressed in flash, saving a little memory space for the application. It also requires the data to be uncompressed after a device reset, which lengthens the boot process. The change was made because more applications are sensitive to flash space limits than boot time.
If you prefer the fastest possible boot time, simply change the setting in the DWR System Editor and rebuild the project. Existing projects are not impacted by the change.