This should cause ZERO problems as long as the incoming country stamped the US passport and you return on the US passport...

Do not even mention the 2nd original country passport when you arrive back in the US. It makes little difference as you are a US Citizen. Technically you are not supposed to use a foreign passport to leave/enter the US but you did in fact use the US passport to enter your original home country - so as long as that passport stamp is shown I don't think you will have an issue.

Lesson here is; next time pay an expediter or service to get you a real passport quicker (NOT an emergency passport), many countries like Taiwan have the 6 month rule - although in the case of Taiwan US citizen can be still arrive with passports shorter than 6 months validity you just need to pay for a landing visa (expensive). Most airlines will let you fly if you sign an indemnity release (we did this for one our guys flying to Taiwan and Cathay Pacific handled it well)