Garth,
It looks like you found the quick start guide in the SDK package. I'm pretty sure your using SDK 1.1.0.3, but correct me if i'm wrong. I'll also attach the guide here for reference. (Please visit the site to view this file)
The Section "Flashing Binaries to SPI Flash on ICE V1/V2 Using CCS" covers the process of flashing a binary.
Can you provide your DIP settings. I beleive we will want to boot from SPI-Flash first.
They are described in the ICEv2 Wiki below.http://processors.wiki.ti.com/index.php/AM335x_Industrial_Communication_Engine_EVM_Rev2_1_HW_User_Guide#Configuration.2FSetup
Also the you said that you are loading spi_flasher.out. Try using the "isdk_spi_flasher.out" spi flasher utility it is found in the sdk folder. Here is my path, which should be the path if you used the defaults.
C:\TI\am335x_sysbios_ind_sdk_1.1.0.3\sdk\tools\flashing tools\SPI_Flash\pre_built\CCS_based
Also what binary are you trying to flash? Can you try using one of the pre-builts that ship with the sdk.