1. A company that is highly disorganized.
2. A company that is shady.
Roughly, I would associate the first with newness or recent high growth. I would associate the second with an established ongoing concern. Neither inspires full confidence in regard to getting paid fully and on time.
That said, it's really more of a spectrum. There are established slow growing companies that are highly disorganized. There are new fast growing companies that are shady. Pre-recession I worked for a Fortune 100 corporation expanding in pace with the housing bubble. The hiring process was more chaotic than it might have been in other economic times.
Having interviewed with and researched the company, there should be some basis for evaluating where on the spectrum it falls. My advice is to go with your gut and I suggest that continuing to explore other employment options is worth consideration even if the contract is acceptable and you go to work there.
Good luck.