I really connected with how you said you are feeling because it is how I have been feeling. I work for a small innovation group (not a startup), so my work environment is flexible. I am also trying to bootstrap a startup project in my free time.
I will have days that I am super productive and can get through a ton of work, but then I have other days that I just can't bring myself to work. It feels weird cause when I force myself to work I get way less done, so I then feel like it is pointless cause I get such little done compared to when I am in the mood for the work. I don't really know how I should feel about it cause I feel guilty on the days that I don't get as much done, but it feels like a waste of time and is draining to just sit there and force out a small amount of work.