Maynard,
We have a bug with a patch fixing it, which might be the root cause.
http://processors.wiki.ti.com/index.php/TI81XX_PSP_04.04.00.01_Release_Notes
DVFS/CLOCK: A fix for frequency scaling of ARM not working issue ( SDCM00089416) is available as a patch over the release package for 04.04.00.01. This can be downloaded from ARM PLL frequency change fix
http://arago-project.org/git/projects/?p=linux-omap3.git;a=commitdiff_plain;h=10d3731856fcfe71bbea3b256248f5d4a0974c03;hp=5b847011dceb8e2d323f28aae4e664c6bef65964
Could you try fixing your issue with this patch.
Best regards,
Pavel