Under review
What makes you think the "Thumbs.db" file is the source of the problem ?

I'm asking because some RAR files are not correctly processed by the library Ubooquity uses to decompress them. Decompressing and recompressing them usually solves the problem. So the fact that your comics work after removing the "thumbs.db" file might just result from the recompression step, not the file removal.
That is a good question. I am not 100% sure, that is the case. But of all cbr files that I see that are not processed correctly, about 98% has a thums.db file in it. 1% contains both jpg and png files. And the left over 1%, I have no idea what is wrong with them. But, next time I see a cbr with a thumbs.db, I will just recompress it, I check if the issue is solved.
Did some further testing. As long as the thumbs.db file is present in the cbr file (even when renamed to something else), I get the 'could not open file' message. Rebuilding the cbr does not help. Removing other files from the cbr (causing a rebuild) does not help. But as soon as the thumbs.db file is removed, the file opens. So for me, there is a clear relation to the thumbs.db file. It might be, that anything other than a jpg file inside a cbr file, causes the same issue. That I did not test.
Ubooquity does not care (in theory) about what kind of files are in the archive. It just keeps the ones it identifies as being images (jpeg, png, gif and, in a future version, webp).

If you can, could send me one or a few files that still can't be opened by Ubooquity after recompression ?
Email to: tom ' at ' vaemendis ' dot ' net
I did report the same problem in this topic 4 months ago. I did a rebuild of all my comic files using ComicRack. Ubooquity is faster if you use cbz (zip) instead of cbr (rar) files. So I don't have the original cbr file's that would not open in Ubooquity. But my gut feeling say's Ubooquity has a problem with some older thumbs.db file's. When I put a new thumbs.db file to a cbr of cbz file Ubooquity seems to have no problem.
Mmm, when I convert the cbr to a cbz file, is works. But with approx. 44K of cbr files, I do not feel happy when I need to convert them all. Besides that, all comics that I download, are always in cbr format.
Results are in, but they're not good. Bottom line is that I can't fix the problem.

I have tested the two files you sent me (one containing a "Thumbs.db" file, the other containing only images). Ubooquity failed to open both of them on my PC (Windows 7).
I uncompressed and recompressed both of them with Winrar. After that, both were succesfully imported in Ubooquity.

I really don't think that the "thumbs.db" file is the cause of the problem, as the archive opening fails long before Ubooquity tries to list the contained files. The error I get comes directly from the external library I use to read rar files (same problem Emmanuel had).

The problem is that this library is not maintained anymore and I did not find any alternative library (compression libraries are not the most fun or easy things to write). So there is nothing I can do about it, sorry.

Your options: recompress the files that are not preoperly read. Or convert them to cbz (that's what I do as I don't like using RAR files, they are not an open standard so there are much less tools/libraries to work with them).