I can not duplicate your problem. As seen by the attached views, the trigger level always assumes the last thing loaded. Perhaps you have some YA offsets involved.
First view = 10xmlprimaryload.jpg = file010.xml loaded into primary buffer.
Second view = 09xmlrefload.jpg = file09.xml loaded into Reference buffer.
Third view = both10primaryloadedlast.jpg = file09.xml into ref buffer first, file10.xml into primary buffer last. I believe that the phase shift is due to different trigger level and/or signal variations between captures. These two captures were obtained by placing my finger on the probe tip. This view also demonstrates why I feel that it would be good to separate the vertical offset and V/Div for the two buffers.
See next post for xml files zip attachment (limit of 3 attachments has been exceeded). If we all use these files then we can describe any issues in common detail.
