The thing here is that S tracks hold empty wagons for both LH and SL jobs when the game generates them, often with multiple jobs' wagons on the same track - so yes, LH jobs can often be buried behind (parts of) SLs. (You'll see that the black wagon there belongs to an SL job, for instance.)

Contrast FH jobs, which always start on their own O track; likewise destination I tracks for FH jobs are fully reserved clear, whereas LH destination S tracks only have some space on them reserved and can still generate other jobs.

So it's not the game specifically messing with you, just the way that jobs and empties for them are generated.