Thanks for coming back to me, and sorry for not providing enough info in the first place!

Here's what I did (all within 5 mins): after installing TFV I ran it and changed the Flash version to Linux 10.1.53. Then I checked a site and a Flash video that never previously worked played perfectly!

I then ran CleaN900 and ran the 'autoclean' command. Then I reloaded the same site again but this time the Flash video didn't play - I get a black box where it is situated on the page (as I did before trying TFV).

I've tried a number of things: reinstalling TFV and Adobe Flash itself as well as clearing the browser cache and trying different Flash versions in TFV. TFV reports the new Flash mode fine and doesn't give me any errors, it's just the Flash doesn't play as it did before I ran CleaN900.