Hello Atul, those jobs should be almost exactly the same as far as the scheduler is concerned. The -lnodes syntax gets translated by PBS into select (and place) statement equivalent. The job's schedselect attribute is what the scheduler actually looks at when considering a job to run, and the -lnodes=1:ppn=2" job should have ended up as "schedselect = 1:ncpus=2:mpiprocs=2". The mpiprocs resource is not actually scheduled upon (it just impacts how the $PBS_NODEFILE gets written), so it is really should be the same as far as the scheduler is concerned.
The jobs would also differ in their place resource (-lselect would have defaulted to free, -lnodes to scatter), but since these are just single chunk jobs that should not have mattered.
Please share the full "qstat -f" output for one of each kind of the jobs you mention above, with the command run as root on the PBS server host (or as a different PBS manager, since schedselect does not show up to normal users in qstat -f output).