My Skype history goes back to my setting of 50 using Miranda 0.95.6.17252.
Assuming that you're still having a problem, you're probably going to need to post your full version information report so that someone can see what plugins you are using that might be interfering with that option.
There used to be a bug in Miranda IM -years- ago which would cause your history display not to pay any attention to that number for a few clients. This was usually fixed by running the database checker and marking all messages as read. But back then the bug caused the message window to display all of the contacts history, rather than the limited number like 15-50.
Additionally, try setting it to 50 because 100 might be too many? I might remember reading something at some point about how 50 was the max that was allowed to be displayed for performance reasons. But all of this pertained to the old Miranda IM client before it became Miranda NG. So it may or may not be relevant anymore.