I think a simple option to add a regular expresion (some kind of "mask" to identify folders to ignore) could do the job.
For instance you could ignore all "#recycle" directories.

I think I understand why it happens.
Now I have to find a fix...

I understand how it would be useful for Kindle owners, but it won't happen for the following reasons:

1- It would require a lot of work for an operation which can be done (although not as easily) by downloading the book (usually a small file) and sending it by email with your usual email app or website.

2- This is a Kindle specific feature. I prefer to work on "generic" features that can be used by all devices. Moreover, Amazon hardware and file formats (azw, mobi) are closed and undocumented, working on them is painful.

Sorry.

I have investigated a bit further.
This problem is not new (in fact sorting was broken from the beginning), but I had never noticed it.
It will be fixed in the next version, but it will require the deletion of your current database file.
It's not a complex operation (I'll include detailed explanation with the release) but all your comics/ebooks will have to be scanned again.

Thanks.
I have not had the time to take a look at it yet, but I'll include it in the doc in a few days.