Thanks Jules, as you pointed out I think checking  "Overwrite already existing files" will fix the issue.
Rsr2Png default configuration is set to avoid doing mistakes, so when the target file already exists it is generally not necessary to override it. And safer too. 
RSR can be different pictures from the PNG you use, what if you override them ? So you have to tell RSR2Png: "I know what I am doing, overrwrite already existing files".

I've refreshed the Rsr2Png UI recently  (Rsr2Png 2.3.4), and it is now easier for me to add new features. I think a list of files like in Pattern renamer, and with a comment explaining why a files is not converted,  would be a great improvement. Coming next. 

nruddock, yes there are some RSR which Rsr2Png and P3dO can't read. I know this. I should have fixed it for long but I thought the RSR format was dead so it was not worth spending time on this. Ok, I will fix this too.

About the alpha channel issue. There's a trick. You must use PNG to PNG conversion and set "Fix blank alpha channel". This option is erasing the alpha channel this is the reason why it is onyl available in PNG to PNG mode. It will only erase channels for pictures which transparent alpha, but again for safety reasons I prefer you ask for it rather than being automatic.

Yarp
www.senosoft.com

Yarp - author of P3DO Organizer for Poser