In a serial communication interface with transceivers that run on different clocks, an ACK transmit FIFO is used to track packets transmitted, and an ACK receive queue is used to track ACK bits for received packets. The ACK receive queue contains a number of entries, and training for the transceivers begins transmitting ACK bits from the ACK receive queue once the ACK receive queue has multiple valid ACK bits. When the ACK receive queue is less than a lower threshold, an ACK compensation mechanism sends one or more packets that make the ACK receive queue grow. When the ACK receive queue is more than an upper threshold, the ACK compensation mechanism sends one or more packets that make the ACK receive queue shrink. The combination of the ACK receive queue and the ACK compensation mechanism allow dynamically compensating for the different clocks of the two transceivers.