I've seen this behavior since 2.8 (when I started using krita, still now on 2.9.1) that sporadically the favorite presets reset to default or that the default brushes get added to the first six places they originally were, also the number of favorite presets goes back to its original number. What I usually do is to put 12 brushes in order not to go back and forward to the panel, making the popup palette suffice, all is good until all of a sudden it resets. sometimes takes a few restarts of the program, sometimes is right after the first time I closed. I wonder if there is an extra step I need to do to keep those presets on place or if this is in fact a bug.

I also notice and I don't know if this is related, probably not, that once the pop up palette gets fill with the used colors the color-blocks facing to the corners of the screen aren't clickable (tried with mouse and penpad), this is: trying to go back to those specific colors I click on them and nothing happens nor the palette goes away.

I use Krita on kde4 and kf5, in two different systems respectively both running Archlinux. Any information is much appreciated.

Hi Quiralta.
With regard to the Favorite Presets issue, it's a bug: https://bugs.kde.org/show_bug.cgi?id=344610
As for the color slots not clickable, I can't reproduce the issue on my system (Ubuntu) even if I recall I had a similar concern, a while ago. So, I guess it has been probably solved.
A similar problem, but with the brush presets, has been quickly solved recently by Sven: https://bugs.kde.org/show_bug.cgi?id=345142
Likely with your next update of Krita from your repository, you should get these changes.

Mvowada, thank you for the information, I wasn't sure if there was an extra step to keep those presets on place.

For the unclickable color palette I also suspecting the window manager, although I have the two kdes, settings are similar if not the same, would play around with the settings to see if that improves the situation.