Taking into account that (allegedly) non modified consoles are also being affected, we need to consider what could possibly be detected on modified and non modified consoles, that might indicate a console has been modified.
A few people have mentioned disk speed which I think might be the most likely cause. Suppose that some recent games have an additional bit of code that times how long it takes for the intro screen (for example) to load. If the drive is running slower than before, then that would take longer to load, and indicate a backup is being run.
However, suppose somebody is running that same game (original this time) on a non modified 360, but the disk is a bit grubby. The intro may take longer to load due to the slightly dirty disk (dirty enough to slow the process down, but not too dirty that the box throws up a dirty disk error), and therefore the box is assumed to be modified.
I've heard rumour that Microsoft are unbanning consoles, which probably indicates that whatever method they are using is bit on the flaky side. For anyone who is banned, I would recommend phonin, and trying to get your box unbanned. Deny all knowledge of a modification, and see whether they will unban you. If they do, then we know that they're still unable to specifically detect the modification, and are using methods that give them a rough idea - something that they'd have to stop doing in case they ban non modified consoles again.