Confusing???

I'm not so sure it had anything to do with him thinking that they were setting him up. I think he ran just because he knew he couldn't trust the police.
And as to why they knew that he had the money... I think they were just guessing. He lives out there where the Sheriff was found, and he ran. Who else does that but someone that is guilty? (At least, I bet that is how the cop was thinking.) Plus, by that time I am sure they knew what kind of gun was used to kill the Sheriff and he was looking at Robert's gun with a lot of interest when he was at the cabin. Even smelled it to see if it had been fired recently. (Not that I know whether or not you can really tell if a gun had been fired just be sniffing it.)
The thing that gets me is this: if the Sheriff was working for the Mayor to get rid of Rey and her husband who were blackmailing him with those pictures, and the Sheriff planned on killing them the whole time, then why did he have the payoff money?

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Nice computers don't go down.