The auditing issue appears to be TCOs (tax compliance officers), hired guns by the IRS not allowing the Foreign Resident Tax exclusion. Guys are having to send in flight plans to their attorney to prove the time that they were not over international waters or US airspace. There is no logic to it at all, but when did the IRS ever operate with logic. So it appears that the time one is over international waters or US airspace, one loses the foreign exemption.
Solution? No one seems to have one. Eventually, it will get kicked upstairs to an IRS agent, who has the ability to settle. Settling usually ends up being a lot less than a full out, with attorneys, appeal process.