Quick introduction: I've been using BRU for over three years now and I don't think I can survive without it. I routinely upload many images to my online community and this tool has been an absolute lifesaver ... over time, I've become a rather advanced user by cleaning up filenames and doing some incredible things with BRU.
Running BRU v3.0.0.1 on Windows 10 PC
This didn't used to be a problem until a couple of months ago with an update. I used to be able to do the following:
OLD NAME 1 --> NEW NAME 001
OLD NAME 10 --> (skip)
OLD NAME 2 --> NEW NAME 002
OLD NAME 3 --> NEW NAME 003
OLD NAME 4 --> NEW NAME 004
However, now when I skip a file, it does all sorts of weird things:
1. It skips the auto-numbering sequence
OLD NAME 1 --> NEW NAME 001
OLD NAME 10 --> (skip)
OLD NAME 2 --> NEW NAME 003
OLD NAME 3 --> NEW NAME 004
OLD NAME 4 --> NEW NAME 005
(By the way, usually I first select all files by hitting CTRL+A, and then unselect a file.)
2. It also skips the cursor selection prior to my CTRL+A selection.
For example, if I had "Old Name 4" selected before choosing all files, then it'll skip that as well ...
OLD NAME 1 --> NEW NAME 001
OLD NAME 10 --> (intentionally skipped)
OLD NAME 2 --> NEW NAME 004
OLD NAME 3 --> NEW NAME 005
OLD NAME 4 --> (unintentionally skipped)

I would definitely appreciate your advice, since this is driving me nuts. I checked menu Renaming Options > Retain Autonumber, since that doesn't solve the problem.