I just wonder what exactly do the code embedded in the at91rm9200 for the clocks/Plls. because I have code that work when loaded in the internal ram after reset (via a JTAG probe) but it doesn't work when I put it in an external TWI eeprom and boot on it via internal code (it seems to halt in function like AT91F_InitClocks).

Is it possible to have the source code embedded in the at91rm9200?

First check that the sixth arm vector is conform to the definition defined in the bootRom chapter of the AT91RM9200 datasheet.
The internal bootrom configure the pllb at 96Mhz and so the master clock is 48Mhz.
Before you code modifies the clocks, the system runs at 48 Mhz.
If your code modifies the pll, please refer to the AT91RM9200 errata sheet to avoid the pll switching problems.