Gmail – Can you keep separate Sent folders in Gmail for each of your custom SMTP servers

[Edited, see comments]

In the Mail application you'll want to add a second (or third, etc. if you have more) SMTP account. Then, when composing an email, you can select which account from which you wish to send it. More information:

http://www.macosxhints.com/article.php?story=20010401111133239

I think something is off with your university's mail system. I've tried sending mail using a custom From address and an incorrect password and it's been my experience that Google's mail system tells me that the remote server rejected my credentials via an error message delivered to my Gmail inbox. For example:

Delivery to the following recipient failed permanently:

<email address>

Technical details of permanent failure: Google tried to deliver your message, but it was rejected by the recipient domain. We recommend contacting the other email provider for further information about the cause of this error. The error that the other server returned was: 535 SMTP AUTH failed with the remote server. (state 8).

Two things to try out: 1) Run a quick test in Thunderbird Portable to see what sort of error message might come back from your school's server if you send it incorrect credentials. 2) Contact the IT department and ask them if you should be receiving errors from their system.

It's also possible that you have a filter that archives or deletes messages matching some criterion that Google's errors happen to share. Give your filters a once-over just in case.