Maybe not that exotic when you start explaining, but you said nothing about IMAP in your first message. It makes a difference, as do POP and Exchange.
The first index run with any version of X1 always depends on how much there is to index, and how much time the PC has to do it. One piece of regular advice is to leave it to run overnight to give X1 enough time.
To my mind 48000+ sent emails is asking for trouble, in more way than one. With regular archiving and use of Rules in Outlook I keep my sent box as empty as possible. I prefer to have my replies alongside the messages they relate to. This keeps individual folders manageable, and may make it easier for X1.
But if you want to force X1 to index all those messages, then point X1 at the Sent Items search.
The status line for indexing has never been reliable. It use of "percentage done" is especially misleading.