Have filed both T4s and T5s prepped in TC today (14.1.55674.0) and twice so far the Submission Number has not either copied in automatically as in previous year, nor does a copy/paste always work (it doesn’t seem to select just the number, but also the words).
Not sure if this is CRA, me, or “behaviour by design”…annnoying, not earth-shattering.
It was populating for me until after the last CRA weekend fixes. 
Since then I have been able to copy/paste without issue though.
I suspect that after Taxcycle altered their program after the first round of changes in early January CRA changed something again that is keeping it from populating automatically. Probably something Taxcycle will address at a later date when time permits.
Probably…as I said, annoying but that’s really all once one is used to it.
Consider yourself lucky it’s worked that long.
The Submission Number has not copied automatically for me for about a month now. Half the time, the XML file doesn’t get “populated” either - I have to copy the file location from the left panel and navigate to it and choose it myself. But, I figure it could be worse, and I’m sure TaxCycle will keep tweaking it to work better.
I’ve had no submissions rejected by CRA (so - yay!), although the occasional T4 forces me to review “formatting errors” before allowing me to submit.