I'm not able to replicate the issue on Chrome OS (60.0.3112.80).  

Steps:
1. Load Adobe's about Flash page
2. Change site setting for Flash to "Allow"
3. (This triggers a prompt to reload, and I do)
4. A puzzle piece appears in the url bar (Omnibox), I click on that to "Run all plugins this time."
5. (This also triggers a reload prompt, which I do again)
6. Content plays back (though the puzzle piece icon still appears)

Note: Even when Flash Player is allowed to run, we affirmatively block Flash content that is smaller than 300x400 pixels (~91% of Flash usage was for 1x1 or invisible pixels, used for ads tracking/ viewability, which had severe privacy and security implications).

Tested this issue on Windows 10 with chrome #60.0.3112.90

Steps followed :
=================
1. Load test url = http://get.adobe.com/flashplayer/about/
2. Right clicked on the flash content to enable flash
3. In the omnibox, click on the plugins blocked notification.
4. Click on the "Run all plugins this time"
5. reload the webpage

Observation : Even though the flash content is loaded, there is "plugins blocked notification" displayed in the omnibox. 

Attaching the screen-cast for reference.

llinares@ Could you please look into it and confirm that this is the exact issue you are facing ?

Thank You...

Deleted: 753096.mp4 2.0 MB

	753096.mp4 2.0 MB View Download

@kkaluri 
That is the behavior I am experiencing, and upon further testing, I can confirm this is specific to some flash content. The content at http://get.adobe.com/flashplayer/about/ has a resolution of 792x180 . Would this be blocked by the 300x400 pixels restriction?

Yes, the content would need to be at least 300x400 to run w/ out getting blocked.  The reason for this size boundary has to do with the common form factor for (display) ads versus interactive content (games and videos).

That would explain that. Only one question remains, which is why that content would automatically run when deleting the local state file, but I suppose it might be expected depending on what information that file holds.

Still in Chrome 60 it only runs first Flash movie even if you set Allow flash settings. The workaround is to change the flag  Run all Flash content when Flash settings is set to "allow"  - from Default to Enabled. This is though too technical for most of the users to set manually. The issue was introduced with Version 60.0.3112.90

in response to Flash content that is smaller than 300x400 pixels?

 "the flash is not a image in this case, it's used as part of the calling process"

Based on the primary usage (>90% of total Flash usage was for ads/ tracking), I don't see us lifting restriction on small form factor content.  My recommendation would be to increase the size of the content to be > 300x400 so that it clearly appears in the user's frame (this is also important for making it easy for the user to activate Flash for the site, since that's the click surface where we will provide that option).

 Issue 754255  has been merged into this issue.

[ Based on comment #9, I think this is WAI. Please reopen if someone disagrees ]