When I first got my X, I was having issues syncing my iTunes music to the phone, regardless of HOW I did the transfer. Filenames, artists, albums....all seemed out of whack. I came to discover that the OS is only reading the mp3 tag (I think that's what it's called) of each file. When I import a cd into itunes, itunes usually does a pretty good job with the mp3 tags of all the files. If I right-click a song file and choose "properties" that's where the tag info can be viewed and edited.
As an example, I'll use the song "Free as a bird" by the Beatles. The file exists in 2 different folders on my hard drive. In one folder, it is labeled 17. Beatles - Free as a bird.mp3 (I have numerous folders that I burn to cd's for use in my car, and my car deck doesn't care about the tag info...it just reads the file names). The second copy is 01 - Free As A Bird.mp3 (located within the folder from the ripped "Anthology" albums. If I drag/drop track 17 to my phone, when I browse my music contents, it will show up as track 1 under the album "Anthology Disc 1" Because if I right-click track 17 and look at the tag info, it will be labeled Track #1 / Artist: The Beatles / Album: Anthology Disc 1
That's why your tracks seem out of order. As tedious as this will be...you will have to right-click EVERY file you want to put on your phone, and change its tag info so that it will appear the way you want it to.
I hope some of this made sense...I tried to be as clear as possible. When I first transferred my itunes music to my new phone, several albums were showing up as "unknown album" or artist. Once I changed the properties of the affected folder, everything showed up exactly as it should. I hope this helps.