Yes- there is a difference between you and your wife's conversion- she has made traditional contributions in the past, and this year made a non-deductible contribution, that was rolled to a Roth in a backdoor conversion. This is not a tax-free event, because of the "pro rata rule."
The pro rata rule is an IRS rule that penalizes taxpayers that selectively convert non-deductible IRAs to a Roth IRA. Basically, if you don't get rid of the balances in the traditional account, your backdoor contribution is taxed again. What happens is: the prorated ("pro rata") amount of traditional IRA balances over the total IRA balances before rollover is computed, and that percentage is applied to the amount rollover, the result is taxed.
You can read more about this here: Rollovers of after-tax contributions in retirement plans
