In the Free transform mode, if you click on a handle with either Shift or Alt down, you respectively scale uniformly and scale around the pivot non-uniformly. If you keep both the Alt and Shift keys down before you click, however, to scale uniformly around the pivot, nothing happens. You must click and drag first, then press the 2 keys. Tested on Win 10
Can confirm. In addition, pressing and releasing Shift or Alt (or both) several times while resizing will mess up the pivot position and the proportion with holding Shift.
(I can reproduce this on Ubuntu 14.04 - Krita 4.0.0-beta1.1.appimage)
This bug seems to be fixed in 4.2.6 you can reopen this report if it persists