I think all the hubbub over disclosure is primarily in the health sciences. Pharma companies fund lots of studies at universities, and there's some notion that the funding source skews the resulting findings. If you're being funded by Pfizer, say, and you want to continue to get Pfizer funding, you might not push very hard on things in a study that suggest that a Pfizer product might have alarming side effects, and you might be more willing to speculate about positive effects of a Pfizer product. It's conceivable (but I have no idea) that a company might in some cases block publication of certain types of findings by university researchers. I think it's reasonable to ask people to disclose possible sources of influence on their work. That doesn't mean that industry funded research is necessarily (or even often) compromised, but some bias is a possibility.

I never had corporate funding while I was in academia, so I don't have any personal experience about what kinds of influence that kind of money might have. People in my group at Google do publish (me not so much, though, since most of what I do involves very sensitive data sets), so I have some notion of the kinds of constraints that industry folks are under.