Unfortunately, they are having problems with a law suggested by the most right-wing party and approved in the republic's assembly.
This law was approved because Portugal had a huge increase in immigrants from all over the world and in most cases they applied for a tourist visa (maximum duration of 3 months) but then stayed here without a visa until they got a job.
However, since you showed all the documentation and provided proof of everything, it doesn't make sense for them to reject the visa.
Unfortunately, there must be people in this position who must be very extremist.
As you know, I'm Portuguese, if you think I can help you with something, let me know.
!BBH