There are two separate issues here - the
estimated tax DFAS withholds from your pay, and the
actual tax you pay when you file your tax return the following April.
When it comes to medical special and incentive pays the amount withheld at the time of payment is based on data you give to DFAS (exemptions) and whether or not you're in a combat zone. This amount is an estimate, and is never exactly correct. The IRS isn't involved in that calculation, they don't care, and you probably shouldn't care (much) either.
What actually matters is what goes on the tax return you file with the IRS. When that time comes, the combat zone tax exclusion is very simple: you get a deduction equal to the lesser of
1) all of your taxable .mil income for every month you were deployed
2) the base pay of the most-senior-enlisted-in-service times the number of months you were deployed
At the bottom of the first page of the
military pay tables (pdf) there is this statement:
For the Master Chief Petty Officer of the Navy, Chief Master Sergeant of the AF, Sergeant Major of the Army or Marine Corps or Senior Enlisted Advisor of the JCS, basic pay is $7,738.80. Combat Zone Tax Exclusion for O-1 and above is based on this basic pay rate plus Hostile Fire Pay/Imminent Danger Pay which is $225.00.
Most post-residency military doctors' monthly taxable pay exceeds that figure, so the CZTE is (presently) $7963.80 per month. If you spend one day in a month in a combat zone, you're entitled to the full month.
I was deployed from 25 Dec 2012 to 3 Aug 2013. When I file my 2013 tax return in April 2014, I'll be able to claim an 8 month CZTE, or a $63,710.40 deduction (8 x 7963.80). I received ASP while deployed, I'll receive ISP/MSP in October (not deployed), and I receive VSP and BCP every month. But in the end that timing really doesn't matter, because all the IRS sees is a $63,710.40 deduction.
The exclusion is UNLIMITED for enlisted members and warrant officers, so bonuses they get in combat zones are truly and completely tax free. For officers, the benefit is more limited. I think this is the source of the confusion - we're always hearing about enlisted members timing their re-enlistment to get their bonus tax free, but the rules are different for commissioned officers.
http://militarypay.defense.gov/pay/combatzone_exclusions.html
http://www.irs.gov/uac/Military-Pay-Exclusion-—-Combat-Zone-Service