Thanks for the replies,
I guess the Alexeys explanation of the quick alignment makes sense if only the 3rd step of the alignment is processed.
In response to step-by-step better alignment "low"-"medium"-"high", I guess JMR (Geobit) suggests that information from previous alignments is kept is subsequent alignments.
I'll try to give a better explanation of my two test-runs:
1, I added all the pictures in my picture folder and started the alignment on "high".
Result: 3/5 of the pictures aligned properly and none of the unaligned ones was possible to align using "Align Selected Cameras".
2, I added pictures step by step, just like JMR suggested, in a chronological order (trying to follow a logical order considering the way pictures overlapped - not the order the pictures were taken since my collegue had gone "back-and-forth" between different locations of the conveyor"). I ran a "low" alignment of these pictures (about 80 pictures) , where 90% of them aligned. The rest aligned with the "Align Selected Cameras"- function.
I then added the rest of the pictures in two more steps with new alignments (alining all pictures) in between, in "low". All the pictures but 2 were aligned.
After this, making no further changes to the chunk, I processed the whole alignment all over again in "medium", and after this in "high". All pictures are now aligned in "high".