Any reason why an employer couldn't sponsor two separate Section 127 Plans?

In this case, employer wants to implement a new tuition assistance plan to a narrow and specific (but nondiscriminatory) class of employees.

But employer already has another plan in place.

I don't see a problem with two Section 127 plans as long as all other compliance (reporting, disclosure, etc.) requirements are satisfied.

Am I missing anything?

I think you're okay as long as IRC sec 127(b)(3) is satisfied aggregating the benefits from the two plan, no one employee benefits more than the $5,250 limit of IRC sec 127(a)(2) and each plan separately satisfies the other requirements of IRC sec 127.