I'm going to answer this, because it seems no one here has ever experienced this which seems strange. I found the answer reading through the "driver development" pdf on the Altera site.
The 10.1 IDE tools will automatically recognize where the "_regs.h" file is located if placed in a certain location. The SBT tools will not. You'll need to create an _avalon_sw.tcl file and place it in the same location as the _avalon_hw.tcl. Use the Altera SPI avalon peripheral _avalon_sw.tcl file as an example. In the _avalon_sw.tcl file will be a place where it indicates the location of the "_regs.h" file and rebuild the BSP. This will then allow the BSP generation process to locate the "_regs.h" file. It was that simple.