Yes, if it is pre-tax, then as dmertz says, it would be removed from Box 1 before the W-2 is printed. This is how all the other pre-tax stuff is handled, like health insurance premiums (code DD in box 12), 401(k) contributions (code D in box 12), HSA contributions (code W in box 12), etc. There just isn't a box 12 code for 401(a) contributions.
$25,000 for the Adjusted Gross pay sounds right, so I don't know why $30,000 appears in Box 1.
There isn't an automatic mechanism in TurboTax to deduct this contribution from income, so perhaps you can ask the people generating the W-2s (I assume it's some software product) how to get it out of Box 1.
"I have the 401 (a) listed as NONE in my Payroll item list since it is not listed. " What does this refer to?
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