Sonar did this for me in Producer 8.5 and now also in X2 Producer.
I've been experimenting with a very simple set-up: 2 MIDI tracks, both 8 bars long, one with a MIDI drum groove clip pattern and the other playing a single note driving Omnisphere playing an arpeggiated (tempo-synched) instrument.
If I solo one track or the other, I can loop indefinitely and everything keeps in-synch, verified by switching in the metronome to check. If I allow both tracks to play together, then after a variable number of loop repetitions the tracks go out of sync and it sounds like a mess.
It always seems to be the drums which do this, the Omnisphere track remains rock solid. It doesn't matter whether the MIDI clip is set as a groove clip or not.
Very occasionally it will all hang together and stay in synch, but most often the timing will break down quite quickly.
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Win 7 64, i5-2500, 8GB RAM
Sonar X2 Producer 64
Creamware Pulsar II PCI
Edirol PCR-300