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I know you've stated that it's bad programming but I thought it would be helpful to post a bit more info that I discovered with more testing:
The issue only happens when using interlaced HIGHGFX screenmodes. Standard amiga screenmodes, even interlaced ones are free from this issue. Likewise standard non-interlaced HIGHGFX screenmodes are fine too.
I use 'HIGHGFX Super-High Res Laced' so experience the issue all the time.
I did a quick video showing what happens to the screen when I copy a file across to the SD card - hopefully this make things clearer...
Has anyone else experienced the following issue?
I have an Indi AGA Mk3 - works like a charm and I've had no issues with it for the past year. Recently got an SDBox device (from Amigastore.eu) which also works great.
However there's a strange interaction between the two whenever I read/write from/to an SD card - my screen kind of flickers. It's hard to describe exactly what it does but text/icons on the screen sort of become fuzzy and crawl around a bit. The moment drive access stops so does the flicker. I have the SDBox powered via an external 5v mini USB cable plugged into it's own wall charger so it's not like it's drawing more power from my A1200.
I have tried ticking some of the advanced options in the Indi Prefs to see if they'd have any effect but alas not. Would be nice to figure out a solution as it's pretty annoying.
Thanks.
Thanks, that's been really helpful. I've ordered the fan and also found the floppy drive Y splitter cable on the AmigaKit site and ordered that too. 
Yes the 68030 runs pretty hot too. I've been running my A1200 with no trapdoor at all and also 1cm high rubber feet to help give it a bit more air circulation and I was happy with how it was running. However the Indi has changed all that. I'm running with no top shield now too and I will buy one of those fans off Amazon, they're only £13.50 and it looks like a perfect match looking at your photo. I like the fact that it is supposed to be very quiet too!
Would you mind showing a photo of where/how you powered it from please? Also how did you attach the fan to the Indi - glue? Is it blowing air upwards or downwards onto the chip?
Thanks
I use the same screenmode but with a max of 32 colors, it's more than workable. More colors slows down the Amiga even with my Blizzard 1230 IV.
No problems with the FBlit on my Workbench 3.1.4.
Also to mention I use a Eizo S1933 monitor.
Yes it's lovely and crisp - just very slightly squished vertically on a 16:9 display but I think I can live with it
Sounds like we have fairly similar setups, I have the Blizzard Mk4 030 (with the SCSI add-on) and 3.1.4. I tend to find that anything lower then 64 colours leads to my icons getting messed up after a period of time using workbench. Just tested Fblit and it's working correctly again... no idea what was happening with it earlier as it definitely wasn't working then. ¯\_(ツ)_/¯
Had my A1200 on all day today and noticed some corruption on screen after several hours which suggests it is heat related. Thankfully it disappeared when I enabled the CCKLine Capacitance option. My Amiga gets very warm indeed with the Indi fitted though - it used to run pretty cool before. Do you find that to be the case too? Just a bit concerned that I might need a fan or something as I don't want to stress the board/chips given the age of the machine.
So I persevered some more and finally stumbled upon a screenmode that just worked. HighGFX Super-Hires Laced 1024x768.
It is still slightly stretched horizontally but it's useable for now until I can figure out what the hell I'm doing!
I have noticed that It is eating up a lot of chip ram though. I use Fblit but it doesn't seem to be working as effectively as before. Opening up a window full of icons takes a good chunk of chip ram each time, whereas before I fitted the Indi it was taking it from fast ram as intended.
Does Fblit not work with the Indi?
Could someone please give me some pointers on how to configure this to give a nice non-distorted 16:9 display on my Toshiba TV?
I have tried for hours and can't seem to get something that both fills the screen but also retains a 1:1 pixel ratio. They always end up slightly distorted in one direction or the other. Between selecting an Amiga screenmode and the tweaks you can make to those plus the VGA one on the Indi plus all the other settings it feels like there's billions of combinations and I'm relying on luck to stumble across the right combination.
My TV has a native resolution of 1366x768. I've installed the HighGFX screenmodes. But yeah I just don't seem to be able to get a working combination. 
I have managed to pick a VGA mode and tweaked it to get it to perfectly fill the screen and the aspect ratio is right... but I can't get an Amiga mode that works with it. I've attached a photo of it in case it helps.
I've had a got of the 'live edit' mode too where you move the mouse around... that was a disaster, especially given how imprecise and twitchy my Amiga mouse is.
Maybe I'm going about this all the wrong way but I'm calling it a night for now as I'm really frustrated with it now.
Any help would be much appreciated. Thanks.
