Maybe the glitch is caused by your source video file. Shotcut requires accurate seeking to get good result. But some files are difficult for Shotcut to seek. For example, VFR files can cause the problem you describe. Also, some containers (like TS) are not easily seekable.
As a test, you could try to convert the video file that is at the beginning of your project. Export with the converted file and see if the glitch is solved.