I think I know what the problem is. Yesterday, I was working on Beta-3,
comparing the latest Jeff F lnkscript and my new linkscript to see if I left
out anything important, and noticed that i had forgotten to add an
EXCLUDE_FILE(*.iwram.o) to the .text section. So, the .text section of your
file is probably getting written to the .text section before it gets to the
.iwram section.

I am currently writing regression tests for all the features of devkit
advance, so in the future it will be easier to see when things break.

I think that the maintainability and features of the new lnkscript and
crt0.S will be worth the bugs I've introduced during this beta period ^_^

Hmm, it just occured to me that I could write a tool which parses the output
of nm and gives you a summary of your image that is taylored for the gba
developer. Such a tool could also tell if anything was screwed up, so it
could be used to create my regression tests. I've been looking for a way to
warn the programmer if they are using ewram overlays and multiboot at the
same time! (i've decided that the results are 'undefined')