Where are the major gaps in the recording? What you are posting is showing the bvr files and each one is 30 minutes per your cut and clip.
The green in your BVR is telling me it is a result of a recent change to the structure and will disappear. Those few that are second or so clips are either when you restarted the camera or there is an issue with the camera itself or another setting. Are you running smart codec in the cameras? Maybe a networking issue and the camera itself is going offline? What is the CPU usage and how are your cameras connected within your system - through a router or isolated?
These files are different than the alerts and triggers. You are pulling up the folder files that will show the BVR files. Select the lightning bolt and then the triggers will be showing and not the full BVR files.
When you watch playback is anything actually missing? If not, its a bug not to be concerned with.
I would recommend upgrading to the latest stable version. 5.3.8.17
Some thing is not configured correctly, after you upgrade.
screen shots
1) Blue Iris Setting about tab (black out your license key)
2) Blue iris status (lighting bolt graph, upper left corner) clip storage tab
3) blue Iris status cameras tab
4) Blue iris settings clips and archiving tab , for the NEW folder, stored folder, alerts folder. (three screen shots)
5) on two of the camera prosperities the record tab.