Won't go in all of the way or won't start? If it won't go in all of the way and it isn't the unique OEM bolts, the replacements are probably too long - if they aren't cross-threaded. I had a heck of a time starting one of mine this weekend. Never had a problem finding the hole before. Must be old age.
The OEM bolt will go in just fine when you first start it and then when you get past the skinny part there is a second small thread. Im going to take my top off all the way this week and mess around with it.