Thanks for the report. Independent of any preference/ setting, Chrome actively blocks all small (less than 300x400) form factor Flash content. The reason for this block is that class of content, representing ~90% of Flash impressions, was used predominantly for ads viewability detection (i.e., is the ad visible on the screen), which had significant performance implications, and persistent/ long lived cookies, which has implications to privacy.
The work around, for site developers, would be to expand the content to be > 300x400.