I have lots and lots of experience with biodiesel made from various feedstocks.  I built a portable commercial biodiesel plant and assisted in the operation of it for a few years.   I even sold and delivered a couple semi loads of biodiesel to John Deere for testing of new engines for the European market.  I have also used B99 in everything, including cross country hauls with a Peterbilt.

Here's what I can tell you.  

Biodiesel is an excellant solvent.  Therefore, it will clean your tanks and fuel system when you first switch to using it if the blend is greater than B20.  Once the fuel system including the tanks is clean, then it will run without any issues other than extreme cold weather.  Until then, you will plug filters and have to replace them frequently.  If your supply tanks are dirty before you put the biodiesel in them, you will have trouble for a long time.  Supply tanks can hold a lot of crud in the bottom from years of zero maintenance and the biodiesel will cut it loose and send it down the hose and into the filters.  Run your finger along the inside of a fuel tank that has been used for a long time for petro-diesel and notice the black residue that you rub loose.  That is the kind of stuff the biodiesel is going to be cleaning from your fuel systems.

The good news is that by starting with clean fuel stored in clean (or new) tanks, you will enjoy using biodiesel and it will extend the life of your fuel injectors and pumps because it adds back the lubricity that has been missing since the introduction of "ultra low sulfur" fuel. 

Biodiesel is also a very good emulsifier that will hold the water content of a fuel source in suspension.  It is very important to remove the water content from the fuel with a water separator and manage your fuel tank levels to minimize condensation.  That means keeping tanks filled at night and when equipment is stored.

Much of the bad rap associated with using biodiesel comes from those that ignore the above cautions and use it as they have always managed their fuel supply.  In addition, the quality of the fuel is important.  A lot of biodiesel has been pushed onto the market without being fully processed and cleaned.  If you buy fuel that has not been completely transesterified and/or washed, you will be trying to run your equipment on gunk.  

One last mention is the feedstock the biodiesel is made from.  It is very difficult to produce a quality fuel from restaurant grease.  Similarily, it is difficult to produce a winter fuel from palm oil.  Virgin soybean oil makes a quality fuel for summer use and is very good for year around use if blended during the winter months.  The absolute best biodiesel is made from canola oil, and it will have nearly identical winter flowability as that of ultra low sulfur diesel.

You can run B100 (or B99) without any issues all year long if you follow the guidance I have outlined above.  If you ignore any part of it you will have trouble.  

The bottom line is buy high quality fully processed fuel made from good virgin feedstocks and only use canola based biodiesel in the winter.