This seems to work correctly for me, but I might not understand your steps correctly.
Are you saying that you have that text on the clipboard, and then you press the paste button into an empty Skyline document and you only get one peptide?
I have attached a PowerPoint showing pictures of what I think your steps are.
I see what you mean. If I paste those 2 lines onto the empty element (dotted box) in the Targets view, the paste goes as expected and a new peptide list is created with both of the peptide forms. Same is true if I paste with a sequence-backed protein element selected. A new peptide list gets created with both forms. But if I paste onto an existing list, then only the first form gets added to the list.
Looks like we must be doing some kind of ignoring based on the bare peptide sequence instead of the modified sequence, because when I use this list in the same way, I get only 2 new peptides, the first pasted of each sequence:
IADPEHDHTGFLTEY[Phospho (Y)]VATR[Label:13C(6)15N(4) (R)]
PES[Phospho (ST)]T[Phospho (ST)]IDER
Thanks for the bug report. I am sure it won't take long to fix.