Hey Splazsh the issue you're experience is quite unfortunate.
The information you have provided defintiely is helpful.
Now that we know that the music plays in a different media player we can rule out content as being the issue.
Now one of the things we cant ry doing is re-creating the iTunes library.
When you recreate the iTunes library it will remove all music from iTunes.
To do so
Click Start - Click Music, in your music fold you should see and iTunes folder
Open the itunes folder - in this folder you will see and iTunes Library file if you right click on it and go to properties it should be a .ITL file, you will want to drag that to your desktop and then reopen iTunes
Once iTunes reopens - it should be completely empty, at this point we will want to re-add your music library back in to iTunes and retest to see if the issue is persisting.
It is possible that iTunes has trouble with glitches in the file while other players such as foobar2000 are able to tolerate glitches. You don't hear any minor skips, beeps, fuzz, or anything in foobar2000 at the trouble spot in the song, right?
The fact that you're getting the glitches in so many of your songs is strange, though, so it's really probably not the case. I'm just putting this out there. :)
Hopefully it's not damage in the storage that you keep your songs on! ;)
I had this porblem and fixed it
So I'm geussing that you didn't download the songs from your ipad and got them for free over the internet
1 You might have not fully downloaded the song files and you have to delete them off your itunes or IOS device and re add them
2 There may have been an error when you were putting the songs on your itunes/IOS device in which case, delete and re-add.
If that doesn't work tell me and I'l help you.