I've got an ongoing issue with runs of MyDefrag on drives with... well, pretty much
any fragmented files at all.
It seems, while it runs, it takes fragmented files in very, very small (like 60,000 byte) chunks. Even though the map indicates that the file is only split in, in the worst case, 2 fragments. Other times this has occurred with files in 130 fragments and so on.
I can't figure out why it's doing this. Its internal workings wouldn't usually make a difference to me, except that it makes MyDefrag slooooooow as hell when it runs across one of these files. MyDefrag eats up a whole CPU core, and memory usage begins piling up. I can see the status indicator endlessly rolling off chunks of the file. Moving 60,000 bytes at offset=123456 to LCN=98765... etc.
The odd thing is, on the map, the file it's working on defragmenting flashes on and off the screen. It only appears on the screen when I pause (spacebar), then disappears (goes to black, "free") again when I resume, sometimes flashing on for a brief moment as it churns away with chunks.
It also bugs me that MyDefrag changed its method from defragmenting-on-move to this new, slow method. It used to take all parts of a fragmented file and move it all at once to a new location out of the way. Now, it wastes a lot of time re-fragmenting the file until it gets to its proper place. It often ends up shuffling the same file from zone to zone several times as it goes (hence my long standing recommendation to change the way MyDefrag finds a free spot by searching for the zone the file would likely end up in). And, you guessed it, every time the file gets shuffled, 100% CPU usage and slooooooow chunk by chunk moves.
Figured I'd bring this little issue to light. Otherwise, well... I'm still loving the thing!

edit: A few screenshots to enjoy, of course.