I used only Opera 12.16 64-bit before installing Opera 15 and it imported the bookmarks just fine at the time, but if you have both a (old) 32-bit and a 64-bit profile I suspect that as sgunhouse says it'll fetch the 32-bit version bookmarks and ignore the 64-bit.
Do this to force a new import of data from the profile you want (WARNING: it'll replace any data you already have in Opera 19 AFAIK):
Originally posted by Pesala and adapted by me:
Windows Key + R "<Path to Opera Next or Dev>\launcher.exe" --presto-small-prefs-dir="<Path to Opera Presto profile>" Open the Bookmark Importer from the Speed Dial
You'll find the Presto profile path in Opera menu -> About Opera.