By default omnet uses the repetition counter as the inner most loop (as you already know), but you can define your own repetition counter like:
seed-set= ${myrepetition=0..99}
**.numHosts = ${nh=0..5}
**.packetsPerSecond = ${pps=5,50,500,5000}
Note that you should NOT use the 'repeat' config key here (so omnet will think you are doing only a single repetition) and the seed-set must be the first key with variable def. This way you run each tuple with several different seeds.
Take care during the analysis that you should average your values for different myrepetition values.
Rudolf
ps: actually setting repetition=10 is the same as placing seed-set= ${repetition=0..9} at the end of the config section.