missing our slot by about 2 minutes.
Your slot is an exact time ie time 16 or 43 etc. Did you miss this time by two minutes or do you mean you missed the ATC CTOT tolerance of +10? I assume the latter which means you missed your slot
and the ATCUs allowable tolerance in which they can get you airborne. Your company then re-filed and a new CTOT was allocated which happened to be an hour later than your original. So far so good, nowt strange there.
In my 20+ years in air traffic I have never heard of a "late update penalty", but then given some of the arsey people who work for handling agents (yes, I know they're not all like that but I have met many over the years who have big chips and bad attitudes), that could just have been their spin on it.
I work at an airport in the SW which sees plenty of slots of which a few get missed and it's not uncommon to see new CTOTs come in (as with your case) where a Ready Message has the affect of bringing forward. It's not outside the realms of possibility that another flight had a problem on the same route and missed it's slot/was cancelled which then gave you the vacant CTOT.