Trackstarts are being deleted when cutting a region?

Right now I'm working on a live album and it's the first time I'm working with WaveBurner. I've got several wave files of a gig which I'd like to burn onto a CD.
Everytime when I cut a region (in order to get rid of seconds of crowd noise between two songs which I don't want on the album) my track starting points are being deleted.
I think I'm doing something wrong but I can't find why... I'm working with WaveBurner 1.6.
Thanks in advance.

I think I've already found the problem myself:
For some reason, the track start markers are connected to the 3rd region in the edit window. The problem with this is that (for instance) the first track start marker has a starting point of -37:14 (negative, relative to the starting point of the 3rd region.
Can anyone tell me what the point is for this feature?

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Trackstarts are being deleted when cutting a region?

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