Initially, when I installed Mathematica 10.0, startup on my workstation was within a few seconds (i.e., acceptably fast). However, at some point, possibly coincident with the upgrade to 10.1 but likely not, startup became extremely slow. In particular, the "Formatting Notebook Content" message appeared for about 40 seconds on every startup before the Welcome screen was even displayed. Many other operations which I seem to recall being close to instantaneous, such as opening the documentation notebook for help on a function, also are now frustratingly slow.

There should be no hardware issue. Mathematica is running on a 24 GByte Windows 10 x64 system and off a fast SSD (as it was when it was working well). I have tried erasing all my local config directories; no luck. I have tried uninstalling and reinstalling Mathematica 10.1 from scratch; no luck.

Finally, on forum advice, I collected these statistics:

In[2]:= FE`Evaluate[FEPrivate`$StartTimes]

Out[2]= {"Initializing kernel connections..." -> 0.125, 
 "Initializing cell styles..." -> 0.282, 
 "Initializing fonts..." -> 0.532, "Initializing menus..." -> 0.563, 
 "Initializing defaults notebook..." -> 0.688, 
 "Initializing defaults clipboards..." -> 0.954, 
 "Initializing internal preferences..." -> 1.032, 
 "Initializing kernels..." -> 1.188, 
 "Opening Welcome Screen..." -> 2.469, 
 "Preloading Favorites..." -> 45.157, 
 "Handling CommandLineOptions..." -> 45.36, 
 "Opening Files..." -> 45.36, "Do Startup Action..." -> 45.36, 
 "Closing Splash Screen..." -> 45.579, "Finished" -> 45.579}

This hints that something between Opening Welcome Screen and Preloading Favorites is the culprit.

Any advice? This problem is so painful that it has cut down substantially on my off-the-cuff Mathematica usage.