Interesting...
What mode are you running in that you only see two digits? In the SPEC200 Modern interface you should definitely see three decimal digits between 0.000 and 0.999. Check to see if the analyzer mode is present in the Modern Interface. It should be between the Quant and Scan choices. If it's absent, your instrument is loaded with the education firmware (which would be a manufacturing error). The firmware is field-upgradable so Thermo Tech Support would be able to email the correct firmware to you.
VISIONlite won't add stability but a firmware upgrade might. The big "adds" with VISIONlite are 0.5nm wavelength precision, kinetics software and the ability to store your data.
Have you contacted Thermo's Tech Support group? If your instrument is still under warranty they may want to bring it to the depot to investigate. If the instrument was new in June you are certainly within the warranty window. Assuming that your method is photometric (i.e. absorbance, not scatter) you should not be seeing noise in the second digit at absorbance values below 1A.