Ian, thanks for reporting that. I confirm there is some kind of bug in Shutter Encoder that apparently produces malformed files when rewrapping AVCHD 1080i content. My test material was from a Canon HF G10 which was released in March 2011.
On the test machines below, it played in QuickTime Player but not properly in FCP or Resolve Studio. It would exhibit various problems and failure modes, including skipping, not playing, hanging the app, etc.
Using VLC 3.0.21 it sort of played but would tend to hang for periods. VLC has it's own internal code and bypasses many of the macOS frameworks. Yet even in this case, VLC malfunctions when playing the rewrapped clips.
Resolve lets you disable hardware video decode acceleration, so I tried that but it didn't help. I also tried Shutter Encoder without hardware acceleration, and it also did not help.
I tested doing the same rewrap using the commercial app EditReady ver. 25.3, and it worked well. So it appears to be a problem with Shutter Encoder or how it's using the underlying FFMpeg libraries.
I tested Shutter Encoder ver. 20 on both macOS Tahoe 26.4.1, FCP 12.2, and DaVinci Resolve Studio 20.3.2 on an M1 Ultra Mac Studio.
I also tested the same Shutter Encoder version on FCP 10.8.1 and macOS Ventura 13.7.8 on a 2017 i7 iMac 27. It behaved about the same.
This is a good lesson about transcoding video. You can never assume it will "just work." Any new transcoding pathway requires careful attention and extensive testing.
Since much AVCHD material is interlaced, that introduces the additional issue of meticulously scrutinizing the output to ensure it is still interlaced and behaves as expected during deinterlacing. QuickTime Player automatically tries to deinterlace if it detects interlaced material, but you can't control that. VLC permit turning off deinterlacing or selecting the type of deinterlacing by menus Video > Deinterlace and Video > Deinterlace Mode.
So if the clips rewrapped by Shutter Encoder cause problems in VLC, Resolve Studio (on both Intel and Apple Silicon), and in FCP, the question is whether options are available. In general, I'd suggest EditReady, a high-quality commercial product that is frequently updated.
In the early 2010's, my documentary team had long been aware of the limitations and problems of AVCHD, and by 2012, even a lower-end DSLR like the Canon Rebel T4i (EOS 650D) recorded in easy-to-handle QuickTime .MOV files. It had a 30-minute recording limit per take due to an European tax issue, but that was very minor relative to the advantages.
The Rebel T4i (EOS 650D) actually costs less than the Canon HF G10 camcorder I used back then, which only recorded to AVCHD. So we moved away from the AVCHD camcorders ASAP back then, and I only have some old archival files from that period.