It seems that after upgrade with Helix-gnome updater, the up2date can't recognize newer packages; example, upgrading gnomeicu-0.93-5 (that, indeed, doesn't work for me) with gnomeicu-0.94_helix_1 (NEWER package), up2date will install back gnomeicu-0.93-5 if used.
The packages have different serial/epoch numbers. You can see this by a) looking at the spec files b) running 'rpm -qp --qf "%{SERIAL}" whatever.rpm
And, we don't support updating your system if you have installed packages with the same name as ours from a different vendor.