The debugger will be running an initialisation script which sets up memory so the program code can be downloaded, and also sets up basic things like cpu clocks, disabling watchdog etc.
It may also be setting up chip select etc for the external sram.
You should find the scipt file being used in the project settings on one of the debugger pages.
Once you have located the file have a look through it to see what it is setting up for you.
Cheers
Martin