I noticed that I had to upload an icon serveral times before it was accepted and appeared in the app description.

Was I doing something wrong, is there a bug, or was there just a delay?

I don't think it was a delay because I left some of the packages alone for a reasonably long time between upload attempts, and the icon appeared immediately after the next upload attempt.

In case you need to check logs, my username is the same as here and I was uploading icons for whois and nano-lang today.

BTW, I think what you've done with openrepos is amazing. It's a Drupal site, right? I think it's a good example of what you can achieve with a flexible CMS like Drupal.