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PHP код:

//global at the top of the script:
new LastCheckpoint[MAX_PLAYERS];
new Float:RandomCheckpoints[][] =
{
    {123.145,123.123,123.123},
    {156.156,156.156,156.156}
};
//Where you want to use it:
RandomCheckpoint_goto:
new rand = random(sizeof(RandomCheckpoints));
if(rand == LastCheckpoint[playerid])goto RandomCheckpoint_goto;
LastCheckpoint[playerid] = rand;
SetPlayerCheckpoint(playerid,RandomCheckpoints[rand][0],RandomCheckpoints[rand][1],RandomCheckpoints[rand][2]); 


I don't know if goto is a good solution but try this
If anyone have a better idea how it is solvable without goto please let me know it