With my config file set as follows:
SkipSpeedFinishQueue: Disabled
PauseAfterSkipSpeed: Enabled

My sim switches from speed four to speed one when waking up or finishing work. Finishing any other activity skips to speed 0(paused) as expected. I tried re-downloading Awesome and generating a new config file, deleting scriptCache, removing all other mods and cc, starting a new save file, etc. All other Awesome mod functions work fine and I think the PauseAfterSkipSpeed worked for sleep/work commands in the past? I haven't used AM for a while though, so that could be a false memory.

AM and game version are both 1.57 and I don't have University or IP.

PEBKAC, bug, or working as intended?

The sender, yes. Not existing as in a family emigrating, a homeless sim that gets cleaned up, etc. Presumably just whenever the game deletes a sim for whatever reason(dead sims are fine if they're not deleted). A long visit to China without collecting mail during the trip usually stuffs my sim's inventory with bills and omniplants when they go home, but I think that's just co-incidence as that sim receives a lot of gifts/love notes in general(maxing the charisma skill challenges seems like a bad idea now  ). I can provide an infected save if you want it, it's in barnacle bay though.

Twallan might be a better source of information to be honest, there's a few posts about it on his site, but they're a bit scattered around. This post has some information and an easy way to trigger the omniplant gifts if you want to test it yourself: https://nraas.wikispaces.com/message/view/Chatterbox/58539624#58551384

This isn't caused by awesome mod, it's an EA glitch. It happens when a sim sends you a gift(omniplant) or letter(bills) then stops existing before your sim collects the mail.

Twallan's Overwatch(newest version) will stop it from happening when you collect the mail, but the game still force-shoves them in your inventory if you don't collect the mail manually before leaving a vacation world. If you forget and they spawn anyway, you can use Master Controller to shove them back in the mailbox(click mailbox>nraas) then use "get mail" on the mailbox as normal.

If you don't travel, Overwatch will fix it for you completely, it's just that obnoxious "Oh noes! You forgot to collect the mail while on holiday! Don't worry, I shoved it in your inventory anyway - You're welcome, by the way!" crap that you need to watch for.