Thats very interesting....
We came across this issue recently on a new client setup while on a trial. Previously we had used an individual config and wrapped it up into a full enrolment package, SM Agent and our own software. This time it wasn't working.
We thought this may be because the SM was on a trial. However we tested last week with a normal paid version and had the same issue. We went back and re-ran an enrolment install from a previous client from last year that did work, it isn't working anymore either.
We concluded that something has changed on the config side and they now appear to be single use only, potentially only live and valid for a short period of time. Though we didn't complete the testing to confirm it was time based rather than simply single use.
So yes we have seen this and it seems to be how it works now. It may be worth opening up a case with Meraki about it. Its on our list to look at for our next large enrolment to check this out