Hi Tony,
The FlashProgrammer support relies on the tcl bare-board initialization file for these kind of boards (in special for CS and eLBC controller initialization). The u-boot makes this part a little bit different so you cannot use this scenario: u-boot initialization + CW FP.
But I have a suggestion for you: please use the sram init file from PA\PA_Support\Initialization_Files\QorIQ_P1\P1013DS_init_sram_flash.tcl (and the connect target, not the download one) - basically this will use the L2Cache memory as SRAM (very useful for bring-up and stuff like this when you don;t have the initialization part for DRAM).
Regards,
Marius