Unfortunately I cannot find my old thread on this issue, as it contained extensive tests. But the issue I reported then and that still persists is that Register has difficulties in handling the UL roles of Barista Bartender and Hobby Shop Register.
By default these roles are given to homeless Sims and they are on duty 24/7 when the role object is on a lot without business hours. This still works but when the object is in a venue with closing times the vanilla game handles these role Sims such that they are being hibernated when the shop/venue is closed and pushed back into the world some time before the venue opens. Register, however, leaves these Sims in the world and they wander around the lot or in the world when the venue is closed. This breaks their locked motives and their work uniform and depending on how often they are drawn into high detail mode they will eventually suffer from motive failure.
A temporary workaround is to assign these roles to residents as this seems to refresh the motive-lock at the beginning of a new shift, but this is still a bit erratic.

Added to the register issue page for review.

When you or someone else look into this you might also want to check the new Waiter role that came with ITF. Although I haven't tried this vanilla yet, on my Sim's second visit to Oasis Landing I noticed that all the Waiter plumbots did not turn up anymore at their work place but were scattered around the world. They were still registered in the Register menu, however. It may be that Register didn't register them in the first place because the only message I received on my first visit to OL referred to the bot consignment clerk, no mention of the waiters. But it maybe therefore be that Register is creating a conflict there.

Yes, I am now fairly certain that the Waiter role has similar issues to the Barista and Hobby Shop Register roles. They are also bi-functional: on lots without closing times they work 24/7 in venues like the Future Lounge they are supposed to have shifts. Oasis Landing has two Future Lounges with one waiter each and the link between them and the role object breaks immediately after one day, causing the waiter to stay away from their workplace from then onwards and wander around town with broken motives instead of locked ones.

Okay I was unable to find where the vanilla game hibernates these Sims. EA has their start and end times set to indefinite and their objects don't check the venue close time (because EA sucks). Twallan does have a fix for that in Register though but they aren't pushed home. The barista actually does have code to hibernate if the role is removed but that doesn't appear to ever be triggered. If their motives are no longer locked I would say the role had to be ran though so that's interesting.

I believe the effect you are seeing in the vanilla game, especially with the hobby shop clerks, is the result of the venue closing code. There's a 50% chance by default that a NPC will go home when a venue closes and when a role sim goes home, they hibernate.

You could try using Retuner to edit By Tunable XML \ Sims3.Gameplay.Skills \ Bartending \ kChanceNPCImmediatelyGoesHomeAfterVenueCloses to 100 to make this happen all the time (don't ask why the venue closing code is using the bartending skill path, it's EA). It should take care of the issue but I'll add code to push all role Sims to go home after their shift ends in a future update of Register.

As for the plumbots, I don't see anything amiss in the code but let me know if they constantly don't show up and you get no notices about them being registered.

Ninja - I'll have a closer look at the bots in game.

Just several additional information.
(1) I remember now that in my initial thread I had a test run for several days without Register in the Uni world but placed all barista and hobby shop role Sims under map tags and they always hibernated and returned the next morning with refreshed and locked motives. This was obvious because the MC map tags seem to remove themselves when a Sim leaves the world and I was busy readding it every day.
(2) Another test was In a neighbourhood with a Late Night apartment and Register installed. I then noticed that those role Sims went back to their apartment lot but remained instantiated during the whole night, they never entered the apartment door. The mixologist that was assigned to the same apartment and worked in the same venue, however, hibernated properly and returned the next day coming from the NPC apartment door. The Uni role Sims, btw, actually spent the night standing in the one apartment that was occupied by a resident family and started to behave like (uninvited) guests during the night.
(3) If there is supposed to be a fix already I think that I can report that it doesn't seem to work, because I observe the exact same behaviour that made me report that issue in the first place back then.
(4) Re the waiter bots: on my third visit to Oasis Landing I removed all waiter bots from their objects, reset those food synthesizers with DE and reregistered them. No notices. The bots that worked in the Cafeteria venue remained and their motives stayed locked, while the two that work in the Future Lounges either stood transfixed in some random place or left the world never to return (I had them on AwesomeMod's radar tags then) unless re-registered.

Is it maybe possible as a first temporary solution to exclude those three roles from being handled by Register? Because as funny as it sounds, the way EA handles them seems to work quite fine.

Unfortunately no as Register replaces the entire role manager and is pretty thorough about it's changes. Obviously the code says one thing but it's not producing the right effects. I'll have to debug the issue. Thanks for the extra info.

Hmm. I was unable to reproduce this with the hobby register clerks. With register in they ran to an empty lot when their shift ended and hibernated. Is the issue reproducible in a fresh university world with only Register in for you? I have noticed the bots aren't being reported as registered. I have yet to get around to monitoring their behavior but I will shortly.

Alright the bots for the lounges are indeed broken. Standing in random remote areas of the world was the observed behavior. And I never got notices for the bot clerk and only one for the 3 roles at the cafeteria. Might take me a bit but I'll stuff it with debug code and find the issue.

I haven't tested the barista's but perhaps once I fix this issue they will all act right.