This is an answer to what I believe is occurring now compared to before, and a few ideas about how things could work. I don't think there is a bug that requires a support request and logs posted, but merely that the silly-bot behavior is still silly, just in a different way and not what the OP wants, yet... Maybe this is more of a discussion item, but I think the developer(s) should read what is said since only they can change what happens.
What USED TO happen is:
After finishing an enqueued walk/loot, the bot would walk back to the pokemon closest to the start then catch all the pokemon along the way and end up at the pokemon closest to the destination so while the bot walked the enqueued path about 3 times, you do end up close to the destination.
Now, the NEW 169 behavior is:
After finishing an enqueued walk/loot, the bot starts catching pokemon closest to the destination, but catches every pokemon it saw along the way so eventually ends up back closest pokemon to the start of the walk, and while it only walks the enqueued path twice, it doesn't end up when you told it to walk to, which is the OP's goal of enqueuing a walk, I think.
What a REAL PERSON does is:
Walks the path AND catches/spins (or ignores pokemon/pokestops) along the way as they were walking. Humans DO NOT remember every single pokemon they saw during a 5 block walk (to use the OP's example) and then go catch them, either in reverse order (now) or the same order (before) as they were seen. This makes the bot more thorough than a human but it makes it impossible to actually end up at a purposeful destination unless no pokemon were encountered during the walk, which is rare in a good area.
I think what the OP is wanting is a way to end up at the destination and start catching pokemon that are seen once they arrive and FORGET/IGNORE the pokemon seen along the way. This is what happens if you are riding your bike or diving a car between areas rich in pokemon and don't want to waste time or drive dangerously catching the few along the way. This is also what the OP is simulating by enqueing a walk, waiting for it to happen, then stopping and restarting the bot so it doesn't remember any pokemon it saw while walking.
What I'd propose is keeping the current behavior as a useful bot-like behavior for those who like catching all seen pokemon along a boomerang path, but ADD THE OPTION TO WALK-BUT-FORGET/IGNORE pokemon that were seen along the path and only catch the pokemon if they are seen again after the enqueued walk is over.
An alternative to having another menu option or two (to forget/ignore) to the pokestop-click menu would be to have a checkbox or toggle-button somewhere in the UI while the bot is running, during an enqueued walked or even otherwise, so it doesn't remember any pokemon while the toggle is disengaged, and could be reengaged after the enqueued walk is over. It would be more useful to have the catching/spinning automatically resume upon reaching the destination, but if that's too difficult just adding a toggle would allow a user who wants to sit and watch the bot walk, manually control when catching/spinning is occurring, just like stopping and restart the bot does, now, but without the somewhat dangerous relogging in. The problem is we can't change any of the settings while the bot is running, even though some make sense to be changed while it is running--whether to catch pokemon or spin pokestops being two obvious ones.
Being able to toggle catching/spinning on an off in real time would help people continue to walk to hatch eggs if they're close to having spun or caught the maximum allowed items in a day. The only problem would be that you couldn't turn off both catching and spinning because then there'd be nothing to walk between that would automatically disappear like happens now when you catch a pokemon or spin a pokestop and it becomes unavailable so the bot turns its attention immediately elsewhere.
For me the ultimate goal would be to do things like a human and catch (or ignore) any pokemon seen along the walk while an enqueued walk is taking place. This requires more sophistication, where there is a purposeful walk occurring at the same time as the ad-hoc and opportunistic catch/spin activities, instead of the enqueued walk and the opportunistic activities being mutually exclusive, but it would be the most efficient as the enqueued walk distance is only traveled once, and the pokemon are all caught along the way. Obviously there needs to be a mode where we can walk without the delay of catching/spinning, too, as proposed above.
