Not all Kosher Organisations are Equal
the big ones are less reliable

Rabbi Fienstien explains that a community Kashrus must be completely financially independent.

It is entirely supported by the community [a levy paid by all the members of the community] and the food manufacturers and service providers do not pay a penny for their certification. 

If any financial benefit is derived from providing certification, then the status of the Kashrus org and its standards are compromised, in which case the larger Kosher agencies are likely to be less trustworthy because they are not fearful of any negative consequences. They are like a juggernaut that keeps on moving forward and crushes any memory of their errors, mistakes and shortcomings, whereas the smaller agencies live in fear of being careless or making an error that will almost certainly be used to attack and obliterate them.

This is a translation (original below) of Rabbi Feinstein's Responsa printed in his Sefer, Igros Moshe YD 4, 1:8
I well remember the great Gaon Rabbi Rosenberg. He stood at the helm of the organisation of rabbis providing Kosher supervision, and he declared that communal agencies providing kosher certification must be fully financially independent before being able to legitimately claim any advantage over individual kosher agencies.

If a communal agency receives any payments whatsoever from the establishments they are servicing, even if only to defray the costs of the Mashgichim (supervisors), then they offer no advantage over the individual Rabbonim who are providing similar services.

In fact, it is quite likely that the Hashgocha of the communal agency is inferior simply because there is no one single individual in whom the final responsibility rests. There is no one "at the top" who feels personally responsible. Whereas an individual Rov is far more likely to feel the responsibility and the repercussions of any errors and he is far more likely to be fearful of having erred, having caused others to sin and lose the respect of his supporters.

Besides it is the way of the world that people tend to automatically trust the larger agencies without really checking their operations unlike the individual Rov who is queried and investigated.

I must also add, that those who provide a Hashgocha without actually supervising the processing at the factory, are guilty of misleading people and other inter-personal sins. Even though the food is Kosher, those consuming the product understand that the product has been monitored by the agency and not just "investigated" to determine that the ingredients and processes are acceptably Kosher.