Differences in codon optimization (tRNA availability) and transcription factor binding at promoters is the most likely cause. There can also be differences in innate immune responses.

Varied plaque size can be seen quite often. I think (but this is a guess, I've not done the experiment) that if you are using overnight cultures as your plating cells, some of the bacteria are in "deeper sleep" than others. So if a phage infects a cell that quickly resume growing when plated, it will go through more phage generations than if it infects a cell that is somewhat quiescent and take a little time to revive, hence fewer phage generations since the expression machinery of the host is turned down.

Similar to the efficiency of plating test, a phage you isolate will not infect all hosts the same way (even if they use the same receptors). If a phage produces more virions per infection, it could present larger plaques. Also, other factors that must be considered is phage adsorption to each host tested, timing of lysis (and the bacterial lawn growth vs the phage infection cycle), if the culture media allows for a proper phage diffusion and the most important part, the host itself (even phage to bacteria densities have impact).

Some information that may help you:

Effect of culture media: Article Effect of various bacteriological media on the plaque morpho...

Phage different plaques:

Article Effects of bacteriophage traits on plaque formation

More in-depth reading:

Article Bacteriophage Plaques: Theory and Analysis

Size of the phage will vary due to the difference in the adsorption rate of the phase to that respective host. The rate of infectivity of a phage will vary depending on the host bacteria. This difference is seen due to the change in binding affinity of the phage receptor to a particular bacterial cell, the stronger the diffusion ability of the phage to the bacteria, the bigger is the plaque size