Looks like Makerbot for Desktop 3.4 along with firmware 1.5 should fix a number of these problems. From the Makerbot web site:

3.4 Notes:

MakerBot Desktop 3.4 is intended for use with Fifth Generation Firmware 1.5. For improved experience, please update your firmware.

Bug Fixes and Improvements:

Improved print quality

Bug fix for Digitizer connectivity issues on Windows

Stopped caching imported files with the same name

Added:

Option to manually calibrate the Z-axis offset of Fifth Generation printers

Fifth Generation button-press override for network prints

Post-print photo sharing to Thingiverse

Ability to set a static IP address

Known Issues:

Windows 8.1 installers will be released shortly. Until then, please continue using MakerBot Desktop 3.3.

After a Fifth Generation printer is reset to factory settings, users should power cycle the printer before setting up Wi-Fi

Transformation icons have invisible text labels on Windows

Occasionally when printing digital store items, a print will jump to 100% completion and stop before it begins printing. Please retry these prints.

Some digital store prints will take a longer than usual time to start. Please check your internet connection and try again.


I am particularly impressed that we can now (supposedly) set Z-home manually. It appears they're admitting that the automated homing using the hall effect sensor in the smart extruder doesn't work as well in real life as it was intended when it was conceived. Obvious somebody noticed that they hadn't thought to test 3.3 with their own Digitizer 3D scanner