Untracked working tree files

I often get this (running git 1.5.6.rc0 presently):

y:/usr/src/git26> git-checkout linux-next
error: Untracked working tree file 'arch/x86/kernel/apic.c' would be overwritten by merge.

which screws things up.  I fix it by removing the offending file, which
gets irritating because git bails out after the first such instance, so
I need to rerun git-checkout once per file (there are sometimes tens of them).

Should this be happening?  I don't know what causes it, really.  All
I've been doing in that directory is running `git-checkout' against
various maintainers' trees.  95% of the time this works OK but
eventually git seems to get all confused and the above happens.

Is there some way in which I can work around this with a single command
rather than having to run git-checkout once per offending file?  I
suppose a good old `rm -rf *' would do it...

Thanks.