Settings → General → Checkout style: was set to multi page checkout. Nothing happened despite using ?cc to clear the cache. Until the next day. We decided we dont' like it and are potentially losing sales right now because it's broken, but changing it back to One-page checkout has no effect… hopefully we can wait for it to magically change again but this is really frustrating why does a setting not take effect?
In addition I can no longer turn customization mode on it says the setting takes effect but it doesn't.
I also set live mode and it shows it as on but it shows Live Mode there after additionaly page loads rather than a button to switch to development mode.
Starting to sound like a permissions related problem to me, i would double check all directory & file permissions to be certain this is not causing issues.
Also, you can manually delete the entire /var/cache and /var/compiled directories to be absolutely certain your cache was cleared, these directories will immediately start to rebuild as you visit your site.
I checked the folders… what ended up fixing it was closing the store and opening it again… also ?cc doesn't seem to work all the time and I have to enable then disable customization mode to see the changes 
Thanks for the help though struck
No problem Atrix, glad you got things moving forward!