I did mergemaster -p previously, my issue was resolved with this svn commit fixing the build prefix in mergemaster:

Thanks for the suggestion though.
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brad davison wrote:
> Greetings. I have updated to 7.1 from a 6.2 box. Kernel built and
> installed successfully, world built successfully, however mergemaster is
> failing:
> $ mergemaster
> *** Unable to find mtree database. Skipping auto-upgrade.

I may be stating the obvious, but being before the /installworld/ shouldn't that be a '/mergemaster -p/' and not just /mergemaster/? From the FreeBSD Handbook: After installkernel finishes successfully, you should boot in single user mode (i.e. using boot -s from the loader prompt). Then run:
# mount -a -t ufs
# mergemaster -p
# cd /usr/src
# make installworld
# mergemaster
# reboot
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