That 100 tx cap is not between two blocks they mine, it is for every hour.
A maximum of 100 TXs submitted can be accelerated every hour.
Don't know at what time they reset this count but i think its UTC time.
EDIT: Timezone confirmed, their counter reset on every hour. I have just included one transaction (some random one)
That would match my experience of just last night. I tried to accelerate a small transaction that had been unconfirmed for 11 hours, but ViaBTC gave me the error message. I then waited until 30 seconds after 11:00 PM (US ET) and tried again.
"Acceleration succeeded"
And it was confirmed on the second block afterwards.
So, it looks like to get an acceleration using ViaBTC's service, the way to do it is to try just after the top of the hour.