Odd behaviour only on one project

Hi,
I am using an Akai MPC1000 sequencer to trigger Superior Drummer and Halion in Cubase. When I mix down audio, I do a real time export so that the sequencer sends the appropriate midi notes to the VSTs.

Everything syncs up fine and I was having no problems until today.

With one of my projects, when I play back the project (including the sequencer simultaneously), everything is lining up and all the notes are in their proper place.

However, when I do a real-time export, there is a slight lag before Cubase starts to play compared to the sequencer. This results in the samples triggered by midi being about a quarter of a bar ahead of the audio tracks.

I have checked on my other projects and this is not the behaviour: the output after real-time export is the same as when I just press play.

I have no idea why on this one project there is a slight lag in the audio before it starts to play, whereas the midi-triggered samples begin immediately after I hit real-time export. To reiterate, this is not the case when I just play back the project.

I am aware of solutions such as just laying down the midi track within Cubase 8, or rendering the midi tracks before doing an export.

However, I just want to know why there is a lag *on one project*. I would have assumed this would be across projects, but it only occurs on one.

Is there some setting I might have accidentally turned on/off?

Here's a short video demonstrating the problem. I can't figure out what is going on. If you keep count with the meter in the first bit of the video, you'll see what I mean about it being in sync. In the second part, you'll see Cubase running slower than the sequencer.