Well, it won’t be easy to find but I’d bet it is a conflict with some other app. It can be misbehaving app but also a bug which doesn’t occur immediatelly after app start. I’d boot, start MEW and leave it running all the day. Work as usual and in regular intervals switch to MEW and try to record macro. When the problem occurs, try to remember what you did since last try, boot and try to reproduce more closely. I know it is tedious and may not have results at all but currently I don’t see any way how to detect the problem better.
I’m stil not quite sure about your symptoms — do you encounter desktop lockup or MEW lockup?