Was able to fix spell cooldowns, however in doing so I had to neuter the debuff display functionality by ripping out a bunch of spell IDs that no longer exist.
Here's how you can fix it yourself:
1) Extract SexyCooldown onto your desktop. Do not extract it to the WoW\Interface\Addons folder yet because we cannot easily edit them from there on Vista/Windows 7.
2) Open up Spells.lua (it's in the Modules folder) in Notepad. You will have to click on the drop down that says Text Documents (*.txt) and select All Files first to get Notepad to display .lua files.
3)Look for GetSpellName, it's around 10 lines from the top. Change that to GetSpellBookItemName. (Renaming such a frequently used function... nice one Blizzard).
4) The line right after that is "if not name then break end". After THAT line, paste the following.
if (GetSpellLink(i, book)) then
5) A few lines after that is an "end". Stick another one right after that so you have "end end".
6) Open up the file Modules\RaidDebuffs.lua. Remove everything between the brackets for RAID_DEBUFF_BLEED, RAID_DEBUFF_MAJOR_ARMOR, RAID_DEBUFF_SPELL_HIT, RAID_DEBUFF_MORTAL_STRIKE. Don't remove the actual headers or the brackets, just the list of numbers inside of them. This will kill SexyCooldown's ability to monitor those debuffs.
7) Save those two files. Move the SexyCooldown folder you extracted on your desktop to its usual location in the Addons folder.
After doing this, SexyCooldowns should work fine. I haven't tested it much but it seemed to recognize the few spells I tried, including new spells. Don't know yet about items or other non-spell cooldowns.