It's been a while since I've been using the SDL Trados Studio 2014 Alignment function. However, I noticed that it is never able to align all the strings (actually, it usually skips a lot of them).
It is very unlikely that it skips segments. You probably think it does this because you did not export all segments.
However, even having only 1:1 perfect connections, when I ask the program to import the alignment to the Translation Memory, it only imports like 70% of the strings or so.
This is probably because you used the "Advanced Import" and did not adjust the Alignment Quality value, which by default is set to 70%.
Or you did not connect the segments in the Alignment Editor.