Well, I think we need to know a lot more about your setup.
Is this with every song?
Is this with songs that only use RealTracks?
Is this with songs that only use MIDI?
Does the stuttering effect play for every instrument in sequence or only some instruments?
Where is the beginning of the end of the songs? 1 bar before the end, 4 bars before the end?
Does the stuttering remain continuous for the duration of the end of the song or progressively get worse, better?
Can you create an audio file of the song and attach it here so we could review?
I think this will be related to the Audio setup on your computer. Which Audio Driver are you using (MME, ASIO, WAS)? (Options > MIDI/Audio Driver Setup).
Please also refer to this post which may assist.