Steps I took to prepare test file:
(Source file: 1920x1080 60fps)
Just one clip on V1
Split on timeline, now you have Clip A & Clip B
Make transition
Saved to mlt file, closed/reopen Shotcut, opened saved mlt file.
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Snapping on.
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Click on transition, holding down left mouse button drag transition just over Clip A, this gives you an offset length.
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Going over Clip B gives you a different length for some reason. I chose to work with :55 frames.
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Lift the transition (right click, Lift)
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Move clip B to the right :55 frames (yes, this widens the gap)
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Grab right side of Clip A and drag to left side of Clip B.
Shotcut 18.09.16 (64 Bit)
Windows 10 Home
Edit:
I split another section on the timeline, this time when I moved the transition (to find the length), I got the same length on both sides. File was not saved and re-opened.