Tried to replicate the issue with no avail. Made a test doc and docx in LibreOffice containing multiple identical and mixed character styles. Then Drag'n'Drop the doc and docx files directly into new ID document's text frames. Word formatting was kept and like expected due to formatting some fonts with additional bold and italic styles, there were several font styles missing, but not a single font style showed up multiple times.
Selected all fonts (the missing and available ones) in the Find Font dialog and replaced them all at once with Minion Pro Regular (installed on system). Works without issues.
Could it be some special version of Word file (PC or Mac)? I could try with MS Word 2016 PC or Word 2008 Mac, but it most likely seems to be weird formatted word files you're trying to import into ID that are causing the issue. To track the issue down, I think we'd need to find out under which circumstances Word files are generating multiple instances of same fonts in ID.
Other not very likely ideas:
Could it be the ID template? Did you try this with an empty ID document, too?
Did you try wiping all font caches, especially those of ID, manually or with FontNuke or maybe with the help of Suitcase that I believe you're using?
When I get into work today I will see about posting up the relevant files.
Some background:
• Word files are sent to the person who processes our legals. Typically these are done on PC by people working for lawyers, city government or small businesses. That can mean a wide range of Word versions. Typically we get DOCX though. Notices of Hearing, Summons, Notice to Creditors, etc.
• Files are processed on a PowerMac G5 running Word 2004. Any styles in the Word file are left alone.
• Files are then placed on server (Windows 2012 server).
• I have a 8.5" x 11" INDT template document with guides laid out for 1 column, 2 column and 3 column width for our newspaper. This allows me to size down any tables that are imported to the correct column width. The template has one master text frame and other than our legals styles has no other styles.
• When I import these documents into the template I have it set to convert any Word styles to our Legal styles. I'm using Adobe CC 2017 on a Mac Pro running OS X 10.10.something and the template was created from scratch.
This last bullet point may be the problem. Due to the variety of outside documents we receive it's never possible to guarantee a direct one to one conversion of styles. Asking the person up front to format the documents so this could happen would only result in additional load upon her and a mess on my end, culminating in phone calls from lawyers wondering where all their bolding and italics went.
I then make sure the text is 5pt with 5pt leading, black, with black underlines. I remove any hyperlinks and I trash all Word styles imported telling ID to retain the formatting (because I need the bolds and italics). I then change the fonts. That's where the problem comes in.
Once I have it all formatted only then do I copy it and paste it into our main legal document.
If I did a direct import I would have a list of styles and colors several miles long because no one who sends these documents to us ever uses the same style twice or names them the same. As anything in the legal document goes into the main newspaper document at some point this can cause serious problems.