If lack of progress is what causes negative emotions, then it seems to me that another possible reason why startup founders might have mood swings is that they usually build one startup at a time. Therefore, if you are not making any progress, you are not making any progress at all. John Conway advises that mathematicians should work at several problems at once in order to avoid such mood swings:

Work at several problems at a time. If you only work on one problem and get stuck, you might get depressed. It is nice to have an easier back-up problem. The back-up problem will work as an anti-depressant and will allow you to go back to your difficult problem in a better mood. John told me that for him the best approach is to juggle six problems at a time.

Startup founders may not have such luxury, but perhaps at least in some cases it is possible to structure things in a similarly disjunctive way, where you can note the problems in a part A, but avoid despair by noticing that at least you are making progress in part B (of course, if different people are responsible for parts A and B, the problem might remain for each one of them). Averaging might make your progress look closer to linear in a certain sense.