Tax question HELP!!!

Ok, just returned back from my tax lady tonight and of course I felt probed once again and owe the gov to much money; however, I ran into a dillema this year and maybe someone on here can help me.

1. I am in sales and I use my personal automobile for transportation to job site sites, sales calls, etc. I use my personal truck, I have a car allowance but that is just added into my check so has nothing to do with exemptions etc.
2. Previous years I have been able to use my mileage as a tax deduction and this year for some reason she said I cannot use it because I have a gas card and they pay for my gas.
3. I did some searching on the net and found an explanation here http://www.irs.gov/pub/irs-pdf/p463.pdf that states I can claim mileage even if I am reibursed. If I don't claim mileage I can claim wear and tear, tires, oil change etc.
Does anyone have any expertise here? Thanks