Logic Pro 10.1.1 comp takes misalligned

Hi,

I am having a bizarre problem when I'm tracking comp takes. Some of the takes are misaligned, creating a jarring out of sync effect on playback. I have checked the recording delay in preferences, it is set to 0. I tried changing the I/O buffer size, it doesn't affect this. The strange thing is that most of the takes are in time, it is only some of them that exhibit this problem. Nothing was changed between takes, some of them are just severely late.

I've attached a screen shot of this. The top two takes, take 5 and take 6 are clearly behind the other ones. They are consistently behind for the duration of the take.

I'm using a Focusrite Saphire Pro 40, set to low latency recording. Input monitoring is disabled on Logic. I've recorded many times with this interface, and it's only recently that this has become a problem. It might have become a problem after updating to Logic 10.1.1, though I can't be sure. I've been using Logic 10 for months, and have never had this problem before.

I can unpack the take, and drag the 2 misaligned ones, but this is pretty frustrating.

Any help would be much appreciated.

Thanks much,

Jeff

Logic 10.1.1, MacBook Pro mid 2009, Mavericks 10.9.5, 8GB ram, 1TB hard drive, Intel 2.26Ghz Core 2 Duo