I've had this problem before...to my best recollection, this is how you solve it (you'll need
ModPlug Tracker; refer to the handy-dandy attached pictures, too):
1) Open the .it file in ModPlug Tracker. Click on the Patterns tab.
2) You should see a row of numbers (see picture #1). After the first number (typically 0) fill in the rest of the boxes with a 1, but don't touch the boxes with "..." in them. Select the second pattern by clicking the box immediately to the right of the box with the "0" in it. It should automatically scroll to the point where the first and second patterns meet.
3) You'll see a number of grayed-out rows (the first pattern), and then a number of normal rows (the second pattern). If there is anything other than a blank in the first row of the second pattern (like in picture #2), clear the row by right-clicking and selecting "Delete Row". The pattern should then be blank, like in picture #3.
4) The .it should now play all the way through without restarting.
By the way, you can test the results at any time by playing the .it in the Tracker. I don't know if this will work in your situation, but it works for me (I did .mp3 -> .wav -> .it -> .umx).
[EDIT]
This might help, too:
http://www.ataricommunity.com/forums/showthread.php?s=&threadid=329057
