This is actually something that was unintentionally added into MediaShout 6.3.80. It automatically applies a small Fade to the cue when going from cue to cue (not from page to page within the cue though).
If this is a large issue, you can roll back to an older build that does not have that Fade. https://s3.amazonaws.com/ms6/MS6_B74.exe
Just make sure to uninstall MediaShout 6 first.
I apologize for the inconvenience this has created.