Storage Library location

So could the compact/rearrange occur during the first eval ? I am not sure if this is the problem, as even if I reboot and try to eval the code later it still fails. So what I was doing originally was

1. Save bootloader from IDE (not using Save on Send so should be all in RAM ?)
   
2. Bootloader runs code ver 1 by eval (This was previously written to storage by bootloader)
   
3. Code ver is running, is notified of software update so reboots to bootloader (E.enableWatchdog(1); while(1);)
   
4. Bootloader receives code v2 via serial port, writes to Storage
   
5. Bootloader eval code v2 but fails due to code errors. Even if I reboot it still fails.
   
   

If I delete code v1 before writing v2 to Storage, it works. Not sure if that shows something I am missing.

I will try your suggestion of eval to RAM as well