I walked into town and the guards arrested me for stolen property (despite not having any items in my inventory with the "stolen" symbol). Then when I did my jail time and looked in the evidence chest there was nothing there.

What happened? Did this happen because (at some point) I picked up some gold that was not to be taken?

How do you know they arrested you for stealing? If you are basing it only on their line "Your stolen goods are forfeit," they say that to you whenever they arrest you regardless of the crime.

Regardless, your thinking about gold could be the case. If you open a 'red' container and take any gold, that is stealing even though the gold in your inventory has no way of indicating which, if any of it, is stolen.

Another cue you can use to help ferret out why you may have been arrested is to anolyze what your bounty was (if you recall) and try and fit it to the table of crimes here: http://www.uesp.net/wiki/Oblivion:Crime

I generally try pretty hard to avoid unpleasant run-ins with the Legion, so folks here who are more adept at thievery and crime in Cyrodiil may be able to help more.