Seems to be consensus in regs that it's annual, cumulative within an account. The Q I could never get answered was if all IRAs (eg: Standard and Roth) had to be taken together within a tax ID number or if they stood alone
If you're with Scottrade, they don't do anything for you on this one. You can cross the $1k threshold and probably never have an issue, at least until the IRS comes knocking for some other reason and then finds the UBTI issue. I'd resolved to take my chances given that you have to file for an EIN for the IRA and then take a withdrawl (w/penalty & withholding to add insult to injury) to pay the tax with the form 990.