Regarding to the developer's mailing list, many Ubuntu/Debian/Fedora/Slackware users ran into heavy trouble, when upgrading from 1.4 to 1.6: http://ml.mate-desktop.org/pipermail/mate-dev/2013-April/thread.html
The problem is a lack of testing after such a long period. However, it mainly seems to affect configurations. The issue is adressed and should be fixed in the next days/weeks.
