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please see for reference the text of the Convention - http://www.irs.gov/pub/irs-trty/swiss.pdf - page 30:
ARTICLE 19 Government Service and Social Security
1. a) Salaries, wages and other similar remuneration, other than a pension, paid by a Contracting State or a political subdivision or a local authority thereof to an individual in respect of services rendered to that State or subdivision or authority shall be taxable only in that State.
b) However, such salaries, wages and other similar remuneration shall be taxable only in the other Contracting State if the services are rendered in that State and the individual is a resident of that State who:
i) is a national of that State; or
ii) did not become a resident of that State solely for the purpose of rendering the services.
So - if you either did not render services in the US or are not a US resident for tax purposes - your compensation should be taxed in Swiss only.
See also the IRS publication 901 - http://www.irs.gov/pub/irs-pdf/p901.pdf - page 32:
Income, other than a pension, paid by Switzerland or its political subdivisions or local authorities to an individual for services performed for the paying governmental body is exempt from U.S. income tax. However, the exemption does not apply to payments for services performed in the United States by a resident of the United States who either:
-- Is a U.S. citizen, or
-- Did not become a U.S. resident only to perform the services.
Pensions paid by Switzerland for services performed for Switzerland are exempt from U.S. income tax unless the recipient is both a resident and citizen of the United States.
So far - you may claim Tax Treaty exemption because services were performed outside the US.
Let me know if you need any help.
if we read the full paragraph on the page 28,
Wages and Pensions Paid by a Foreign Government. Wages, salaries, pensions, and annuities paid by the governments of the following countries to their residents who are present in the United States as nonresident aliens generally are exempt from U.S. income tax. The conditions under which the income is exempt are stated for each of the countries listed.
As you see that statement do not address US citizens at all... and doesn't contradict the Tax Treaty
Exemption under U.S. tax law. Employees of foreign countries who do not qualify under a tax treaty provision and employees of international organizations should see if they can qualify for exemption under U.S. tax law.
This statement advises to verify the Tax Treaty provision to verify qualification for exemption - that is what we actually did above.
If you work for a foreign government in the United States, your foreign government salary is exempt from U.S. tax if you perform services similar to those performed by U.S. government employees in that foreign country and that foreign government grants an equivalent exemption. If you work for an international organization in the United States, your salary from that source is exempt from U.S. tax.
This statement point to the situation if you were working in the US - it doesn't relate to you.
Honestly I do not see any contradiction, but I understand your concern.
I suggest you to call the IRS hotline for clarification - 1-800-829-1040 and confirm the answer provided.
You may also request a private letter ruling from the IRS to backup your decision.