I've never experienced that personally. I've only got a little over 5000 tracks on mine. There could be a limit to the total number of tracks allowed (and really, based on the overall design if the media playback system, it wouldn't surprise me if there is). If that's the case, maybe MFT has a higher limit than the older sync versions.
If all the tags are ID3, those shouldn't be causing an issue, though check and make sure that both Artist and Album Artist are filled for all. Missing one or the other could cause an issue. Also make sure that none of the artist names are using special characters. I had to rename all my AC/DC songs, because they kept showing up as AC. Avoid / \ -, etc... () seem to work fine, though.
Only other thing I can suggest checking is the actual file name structure your using. Overly long, or complicated (lots of special characters) could be causing the problem. I keep all my files in a very basic file name structure: Artist - Album - Track Title.wma Never had an issue with files named like that.
Beyond that, I'm not sure what else to try. Make sure you got the latest sync version installed... Give it an hour or more to index. The initial index of my 5000 tracks took a good 15-20 minutes to complete and then another 5-10 minutes to build voice commands the first time. Only real way to know it's working is have it play all tracks. Every time you skip to the next track the total number of tracks should keep slowly increasing. 1/2000, 2/2025, 3/2132, etc...
Hope that helps.