The companies spent all the money this year on R&D expenditures. That was cash out of their pocket (they spent it this year, so it reduced this year's cash on hand). The effect of the rollback is that they can now only count 20% of those expenditures to reduce their profits (and, by extension, their taxes) this year, so they are paying taxes this year on the remaining 80%. While yes, the profits are higher, the cash is not any higher, and cash pays the tax bill.

Note, this was not an "unexpected" change (it's been in the code), but it WAS unexpected that the provision was not extended.

Note that this affects not just startups. My wife's firm is a small, employee-owned, non-tech S-corp. This hit them as well. It resulted in tax bills for the shareholders approximately 25-30% greater than the firm's accountants expected them to be. The shareholders are on the hook for those higher taxes, although the company did the right thing and distributed extra cash to them to offset the higher taxes.