The B737-800 (amongst others) has Auto-Brake, which applies maximum braking in the event of a Rejected Takeoff, and Anti-Skid is a normal component of Auto-Brake and Manual braking.
Most aircraft have a speed threshold below which Anti-Skid does not operate, and this is no different on the B737-800. Below this speed, there is no Anti-Skid, and brake locking CAN occur when Maximum braking is applied, leading to considerable juddering. The Auto-Brakes are disengaged by momentarily applying normal manual braking, whereafter modulated manual braking without Anti-Skid can take place. This seems to fit your sequence of events -
"as we braked to come to a stop at the holding point we shook quite violently" - Yes, 'as we came to a stop', i.e. at lower speeds, maximum braking is still being applied without Anti-Skid, some wheel locking / skidding is a distinct posibility.
"the brakes were released and then applied again" - The pilot has depressed the manual brakes, temporarily releasing the Auto-Brake, and then commenced Manual braking.
"and we came to a holt again shaking" - The pilot is now applying manual braking, and modulating it to prevent skidding / wheel locks.
Actually, your description is a pretty accurate depiction of a typical RTO from high speed.
BTW, the reason for the low speed threshold below which the Anti-Skid does not work is to prevent a very undesirable and unwanted 'Anti-Skid commanded' brake release during taxy and ground manoeuvering operations.
Regards,
Old Smokey