Latest development on Ubuntu 12.04:
1. Check the tools in Tools pad. Notice that last two icons are: Ellipse and Freeform Shape.
2. Edit | Add-in Manager.
3. Installed tab | click on rectangle to expand Core.
4. Click on Default Tools and click Disable and then Close button.
5. (If you click Enable button before pressing Close button problem does not appear). Restart Pinta.
6. Repeat steps 2 to 4 and click Enable for step 4.
7. Notice the last tool I see in first column is Text. So two more lines are hidden.
This is probably a problem of small screen in my case 1024 x 768, because Palette pad after disabling Tools and restarting Pinta is maximized = showing all of the colors in palette, so not enough space in Tools.
P.S. This is not a huge problem, tools can be manually resized, but I expect to get the same thing back when I disable and enable again. Maybe mark this bug as Low importance.
I think this was fixed along with bug 1188988. Disabling and re-enabling the core tools extension is working for me now in Pinta 2.2