I had the same issue- no 2nd name of mother on my passport although she uses last name on her passport. Because I was applying alone (without parents). I wrote the same name in First & Second name field AND explained this in the LOE (letter of explanation) that on my passport and other documents my mother has only first name. This way it worked out for me and got the PR without much hassle.
P.S.- I rarely check my email linked with this forum, luckily just checked it & saw your post.
