That is bizarre! If you've had a successful visit and hold a UK visa then it ought to be almost a formality to get the visa!
I hope you get it sorted but the stress and time created by these processes is of the scale.
Perhaps Portugal is clamping down a little as unknown many people who have happily settled there in the past few years as it really does seem to be a lovely place to relocate to.
Best wishes
Thanks it is odd and very bizarre and expect to get this cleared up as soon as possible. Just the hassle like you mentioned as this is another day wasted. Good to hear from you and appreciate it.