You were spot on in your assessment! I changed out a splitter and moved my cable box up a level (probably should have been on the top level anyway) and I am able to decode 98 again. Maybe the cable box was overloading the frontend of the HD Homerun tuner. So my setup is now....
----> Cable Modem
l
----> Cable Box ----> HD Homerun
TWC --->l l
------------------------------>----> HD Homerun
l
----> HD Homerun
l
----> HD Homerun