how many shares do you think JC gave away AKA dilution...
new debt or equity financing arrangements may not be available to us when needed on acceptable terms, if at all. Additionally, these alternatives may require significant cash payments for interest and other costs or could be highly dilutive to our existing shareholders. Any such financing alternatives may not provide us with sufficient funds to meet our long-term capital requirements. If necessary, we may explore strategic transactions that we consider to be in the best interest of us and our shareholders, which may include, without limitation, public or private offerings of debt or equity securities, a rights offering, and other strategic alternatives; however, these options may not ultimately be available or feasible.
No matter what you pull out of the Risk Factors section for JSDA, they are ten times worse for AFFY.
As far as JSDA as a going concern, the statement has been there for some time and is just copy/pasted at this point as CYA. Since the company is close to breakeven, the value of the statement is no longer very important or realistic.